Updated MSU email server specification file

Rainer Fuchs EMBL Data Library fuchs at embl-heidelberg.de
Wed May 4 09:03:32 EST 1994


Included is an up-to-date version of the service specification file used by the
MSU mail server utility program. It now lists 26 email servers; recent additions
include Bioccelerator, BioSCAN, EMBL PROSITE, SBASE, ProDom, and GCRDb.

MSU simplifies access to Internet email servers by providing a customizable menu
interface. MSU is available for UNIX and VAX systems from
{ftp,gopher,www}.embl-heidelberg.de.

-- 

Rainer Fuchs
EMBL Data Library
Fuchs at EMBL-Heidelberg.DE

================================================================================

############################################################
# MSU default service specification file
# Rainer Fuchs, EMBL Data Library
# Fuchs at EMBL-Heidelberg.DE
############################################################


###
# EMBL Blitz server
# 3-Dec-1993
###

service-name:   EMBL BLITZ server    
service-info:   Ultra-fast sequence comparisons on massively parallel computer
service-addr:   blitz at embl-heidelberg.de
--
help-address:   blitz at embl-heidelberg.de
help-body:      help

//

service-prot-options:
start-token:    SEQ
end-token:      END
maxseqlen:      10000
--
msu-object:
obj-name:       Enter search title
obj-info:       This string will be used as the Subject of the return mail
obj-tag:        TITLE
obj-class:      String
maxlen:         60
--
msu-object:
obj-name:       Value of PAM matrix
obj-info:       The amino acid weight matrix used to score non-identical amino acid pairs.
obj-tag:        PAM
obj-class:      Int
min:            1
max:            500
def:            120
--
msu-object:
obj-name:       Enter gap penalty
obj-info:       Score for gaps in alignment
obj-tag:        INDEL
obj-class:      Int
min:            5
max:            30
--
msu-object:
obj-name:       Enter number of best alignments
obj-info:       Number of alignments to show
obj-tag:        ALIGN
obj-class:      Int
min:            1
max:            100
def:            30
--
msu-object:
obj-name:       Enter number of scores
obj-info:       Number of scores to report
obj-tag:        NAMES
obj-class:      Int
min:            1
max:            100
def:            30
// no nuc options


###
# Weizmann BIOCCELERATOR
# 4-Mar-1994
###

service-name:   BIOCCELERATOR
service-info:   BIOCCELERATOR installed at Weizmann Institute of Science, Israel
service-addr:   bicserv at sgbcd.weizmann.ac.il
--
help-address:   bicserv at sgbcd.weizmann.ac.il
help-body:      help

//

service-nuc-options:
start-token:    ..
end-token:      end
seq-format:     ascii
lowercase:      no
maxseqlen:      10000
--
msu-object:
obj-name:       Select SW search
obj-tag:        Bic_sw
obj-mandatory:  y
obj-class:      Fixed
--
msu-object:
obj-name:       Show alignments
obj-info:       Include alignments in output
obj-tag:        align
obj-class:      Boolean
def:            y
--
msu-object:
obj-name:       Label your sequence
obj-info:       Assign a (short) name to your sequence
obj-tag:        begin
obj-class:      String
def:            Untitled
//
service-prot-options:
start-token:    ..
end-token:      end
seq-format:     ascii
lowercase:      no
maxseqlen:      10000
--
msu-object:
obj-name:       Select database
obj-info:       Subset of database to be searched
obj-tag:        Bic_sw
obj-mandatory:  y
obj-class:      Group
elements:       2
def:            1
items:          -Infile2=SWISS:\*, -Infile2=PIR:\*
--
msu-object:
obj-name:       Show alignments
obj-info:       Include alignments in output
obj-tag:        align
obj-class:      Boolean
def:            y
--
msu-object:
obj-name:       Label your sequence
obj-info:       Assign a (short) name to your sequence
obj-tag:        begin
obj-class:      String
def:            Untitled


###
# FLASH
# 5-Oct-1993
###

service-name:   FLASH
service-info:   Ultra-fast seq. comparisons. Registr. req. at dflash at watson.ibm.com 
service-addr:   dflash at watson.ibm.com
service-subject: dflash
--
help-address:   dflash at watson.ibm.com
help-subject:   dflash
help-body:      send help
--
reg-address:    dflash at watson.ibm.com
reg-subject:    Registration
reg-options:
msu-object:
obj-name:       Your name
obj-tag:        Name:
obj-mandatory:  y
obj-class:      String
msu-object:
obj-name:       Your affiliation
obj-tag:        Affiliation:
obj-mandatory:  y
obj-class:      String
msu-object:
obj-name:       Your postal address
obj-tag:        Address:
obj-mandatory:  y
obj-class:      String
msu-object:
obj-name:       Your email address
obj-tag:        Email:
obj-mandatory:  y
obj-class:      String
msu-object:
obj-name:       Your phone number
obj-tag:        Phone:
obj-mandatory:  y
obj-class:      String

//

service-prot-options:
start-token:    BEGIN
end-token:      1
seq-format:     fasta
minseqlen:      30
maxseqlen:      1000
--
msu-object:
obj-name:       Enter PAM scoring matrix or leave blank and select BLOSUM matrix on next
                question 
obj-info:       A value between 10 and 500 in multiples of ten. Higher values are optimal for
                more distantly related sequences; lower values are better for more similar
                sequences. 120 or 250 are good default values.
obj-tag:        PAM
obj-class:      Int
min:            10
max:            500
--
msu-object:
obj-name:       Enter BLOSUM scoring matrix or leave blank if you entered a value for PAM matrix 
obj-info:       A value out of 30,35,40,45,50,55,60,62,65,70,75,80,85,90, or 100. Higher values
                are better for more closely related sequences; lower values are better for
                detecting distant sequence similarity. 62 is a good default.
obj-tag:        BLOSUM
obj-class:      Int
min:            30
max:            100
--
msu-object:
obj-name:       Enter number of best alignments
obj-info:       Number of alignments to show
obj-tag:        ALIGNMENTS
obj-class:      Int
min:            1
max:            10000
def:            10000
--
msu-object:
obj-name:       Enter minimum score to report (threshold)
obj-info:       Only scores higher than the threshold are reported
obj-tag:        THRESHOLD
obj-class:      Int
min:            30
max:            100
def:            50


###
# BioSCAN
# 4-May-1994
###

service-name:   BioSCAN
service-info:   Fast seq. comparisons using special-purpose hardware.
service-addr:   bioscan at cs.unc.edu
--
help-address:   bioscan at cs.unc.edu
help-body:      help

//

service-nuc-options:
start-token:    BEGIN
seq-format:     fasta
--
msu-object:
obj-name:       Program name
obj-tag:        PROGRAM bscan
obj-mandatory:  y
obj-class:      Fixed
--
msu-object:
obj-name:       Select database
obj-info:       Subset of database to be searched
obj-tag:        DATALIB
obj-mandatory:  y
obj-class:      Group
elements:       15
def:            1
items:          gb,gbbct,gbest,gbinv,gbmam,gbpat,gbphg,gbpln,gbpri,gbrna,
                gbrod,gbsyn,gbuna,gbvrl,gbvrt
--
msu-object:
obj-name:       Report format
obj-info:       Specifies the format in which results will be delivered
obj-tag:        REPORT
obj-class:      Group
elements:       5
def:            1
items:          Segment,Simple,Align,Compress,None
--
msu-object:
obj-name:       Statistical expectation
obj-info:       Cutoff score for reporting hits is calculated from this value
obj-tag:        EXPECT
obj-class:      Float
min:            0.0001
max:            1000
def:            200
--
msu-object:
obj-name:       Substitution scoring matrix
obj-info:       Weight matrix for non-identical residue matches
obj-tag:        MATRIX
obj-class:      Group
elements:       2
def:            1
items:          DPAM47I,BLOSUMN

//
service-prot-options:
start-token:    BEGIN
seq-format:     fasta
--
msu-object:
obj-name:       Program name
obj-tag:        PROGRAM bscan
obj-mandatory:  y
obj-class:      Fixed
--
msu-object:
obj-name:       Select database
obj-info:       Subset of database to be searched
obj-tag:        DATALIB
obj-mandatory:  y
obj-class:      Group
elements:       2
def:            1
items:          sw,pir
--
msu-object:
obj-name:       Report format
obj-info:       Specifies the format in which results will be delivered
obj-tag:        REPORT
obj-class:      Group
elements:       5
def:            1
items:          Segment,Simple,Align,Compress,None
--
msu-object:
obj-name:       Statistical expectation
obj-info:       Cutoff score for reporting hits is calculated from this value
obj-tag:        EXPECT
obj-class:      Float
min:            0.0001
max:            1000
def:            200
--
msu-object:
obj-name:       Substitution scoring matrix
obj-info:       Weight matrix for non-identical residue matches
obj-tag:        MATRIX
obj-class:      Group
elements:       21
def:            4
items:          PAM5,PAM30,PAM70,PAM120,PAM160,PAM180,PAM250,BLOSUM30,BLOSUM35,
                BLOSUM40,BLOSUM45,BLOSUM50,BLOSUM55,BLOSUM62,BLOSUM70,BLOSUM75,
                BLOSUM80,BLOSUM85,BLOSUM90,BLOSUM95,BLOSUM100
--
msu-object:
obj-name:       Apply filter
obj-info:       Eliminates biologically uninteresting reports
obj-tag:        FILTER
obj-class:      Boolean
def:            y


###
# NCBI BLAST
# 7-Oct-1993
###

service-name:   NCBI BLAST
service-info:   BLAST similarity searches at the National Libr. of Medicine
service-addr:   blast at ncbi.nlm.nih.gov
--
help-address:   blast at ncbi.nlm.nih.gov
help-body:      help

//

service-nuc-options:
start-token:    BEGIN
seq-format:     fasta
--
msu-object:
obj-name:       Select program to use
obj-info:       blastn is nucleotide seq vs. nucleotide db,
                blastx is translated nucleotide seq vs. protein db
obj-tag:        PROGRAM
obj-mandatory:  y
obj-class:      Group
elements:       2
def:            1
items:          blastn,blastx
--
msu-object:
obj-name:       Select database
obj-info:       Subset of database to be searched
obj-tag:        DATALIB
obj-mandatory:  y
obj-class:      Group
elements:       18
def:            1
items:          nr, genbank, gbupdate, embl, emblu, pdb, vector,kabatnuc,
                dbest, epd, swissprot,pir,spupdate,genpept,gpupdate,kabatpro,
                tfd,palu
--
msu-object:
obj-name:       Show histogram
obj-info:       Displays histogram of scores
obj-tag:        HISTOGRAM
obj-class:      Group
elements:       2
def:            1
items:          yes,no
--
msu-object:
obj-name:       Enter number of scores (descriptions)
obj-info:       Number of scores to report
obj-tag:        DESCRIPTIONS
obj-class:      Int
min:            1
max:            1000
def:            100
--
msu-object:
obj-name:       Enter number of high-scoring segment pairs (alignments)
obj-info:       Number of high-scoring segment pairs to report
obj-tag:        ALIGNMENTS
obj-class:      Int
min:            1
max:            1000
def:            50
--
msu-object:     
obj-name:       Scoring matrix for BLASTX (LEAVE BLANK FOR BLASTN searches!)
obj-tag:        MATRIX
obj-class:      Group
elements:       4
items:          BLOSUM62,PAM40,PAM120,PAM250
--
msu-object:
obj-name:       Return email address
obj-info:       An alternative email address to which results should be sent
obj-tag:        PATH
obj-class:      String
//
service-prot-options:
start-token:    BEGIN
seq-format:     fasta
--
msu-object:
obj-name:       Select program to use
obj-info:       blastp is protein seq vs. protein db,
                tblastn is protein seq vs. translated nucleotide db
obj-tag:        PROGRAM
obj-mandatory:  y
obj-class:      Group
elements:       2
def:            1
items:          blastp, tblastn
--
msu-object:
obj-name:       Select database
obj-info:       Subset of database to be searched
obj-tag:        DATALIB
obj-mandatory:  y
obj-class:      Group
elements:       18
def:            1
items:          nr,swissprot,pir,spupdate,genpept,gpupdate,pdb,kabatpro,
                tfd,palu, genbank, gbupdate, embl, emblu, pdb, vector,kabatnuc,
                dbest, epd
--
msu-object:
obj-name:       Show histogram
obj-info:       Displays histogram of scores
obj-tag:        HISTOGRAM
obj-class:      Group
elements:       2
def:            1
items:          yes,no
--
msu-object:
obj-name:       Enter number of scores (descriptions)
obj-info:       Number of scores to report
obj-tag:        DESCRIPTIONS
obj-class:      Int
min:            1
max:            1000
def:            100
--
msu-object:
obj-name:       Enter number of high-scoring segment pairs (alignments)
obj-info:       Number of high-scoring segment pairs to report
obj-tag:        ALIGNMENTS
obj-class:      Int
min:            1
max:            1000
def:            50
--
msu-object:     
obj-name:       Scoring matrix applied for sequence comparisons
obj-tag:        MATRIX
obj-class:      Group
elements:       4
items:          BLOSUM62,PAM40,PAM120,PAM250
--
msu-object:
obj-name:       Apply filter
obj-info:       Eliminates biologically uninteresting reports
obj-tag:        FILTER
obj-class:      Boolean
def:            y
--
msu-object:
obj-name:       Return email address
obj-info:       An alternative email address to which results should be sent
obj-tag:        PATH
obj-class:      String


####
# EMBL FASTA server
# 4-Oct-1993
###

service-name:   EMBL FASTA server    
service-info:   Protein and nucleotide database searches using the FASTA algorithm
service-addr:   fasta at embl-heidelberg.de
--
help-address:   fasta at embl-heidelberg.de
help-body:      help

//

service-nuc-options:
start-token:    SEQ
end-token:      END
maxseqlen:      32000
--
msu-object:
obj-name:       Select database
obj-info:       Subset of database to be searched
obj-tag:        LIB
obj-class:      Group
elements:       20
def:            1
items:          EMALL,EMNEW,EFUN,EINV,EMAM,EORG,EPHG,EPLN,EPRI,EPRO,EROD,ESYN,EUNA,EVRL,
                EVRT,GBNEW,GBALL,GBONLY, GENEMBL, GENEW
--
msu-object:
obj-name:       Enter k-tupel value (word size)
obj-info:       Controls the sensitivity of search. The lower the case the more sensitive
                the search, but also the longer the execution time
obj-tag:        WORD
obj-class:      Int
min:            3
max:            6
def:            6
--
msu-object:
obj-name:       Enter number of scores
obj-info:       Number of scores to report
obj-tag:        LIST
obj-class:      Int
min:            1
max:            100
def:            50
--
msu-object:
obj-name:       Enter number of best alignments
obj-info:       Number of alignments to report
obj-tag:        ALIGN
obj-class:      Int
min:            1
max:            30
def:            10
--
msu-object:
obj-name:       Search one strand only
obj-info:       Search one strand only. By default, both strands will be searched
obj-tag:        ONE
obj-class:      Boolean
def:            no
--
msu-object:
obj-name:       Enter search title
obj-info:       This string will be used as the Subject of the return mail
obj-tag:        TITLE
obj-class:      String
maxlen:         60
//
service-prot-options:
start-token:    SEQ
end-token:      END
maxseqlen:      32000
--
msu-object:
obj-name:       Select database
obj-info:       Subset of database to be searched
obj-tag:        LIB
obj-class:      Group
elements:       8
def:            1
items:          SWALL, SWNEW, SW, NBRF, PIRONLY, SWISSPIRALL, BROOKHAVEN, NRL
--
msu-object:
obj-name:       Enter k-tupel value (word size)
obj-info:       Controls the sensitivity of search. The lower the case the more sensitive
                the search, but also the longer the execution time
obj-tag:        WORD
obj-class:      Int
min:            1
max:            2
def:            2
--
msu-object:
obj-name:       Enter number of scores
obj-info:       Number of scores to report
obj-tag:        LIST
obj-class:      Int
min:            1
max:            100
def:            50
--
msu-object:
obj-name:       Enter number of best alignments
obj-info:       Number of alignments to report
obj-tag:        ALIGN
obj-class:      Int
min:            1
max:            30
def:            10
--
msu-object:
obj-name:       Enter search title
obj-info:       This string will be used as the Subject of the return mail
obj-tag:        TITLE
obj-class:      String
maxlen:         60


####
# PIR FASTA server
# 6-Oct-1993
###

service-name:   NBRF/PIR FASTA server    
service-info:   Protein database searches using the FASTA algorithm
service-addr:   fileserv at nbrf.georgetown.edu
--
help-address:   fileserv at nbrf.georgetown.edu
help-body:      help search

//

service-nuc-options:
seq-format:     pir
end-token:      END SEARCH
--
msu-object:
obj-name:       Enter k-tupel value (word size)
obj-info:       Controls the sensitivity of search. The lower the case the more sensitive
                the search, but also the longer the execution time
obj-tag:        SEARCH KTUP=
obj-class:      Int
min:            3
max:            6
def:            6
//
service-prot-options:
seq-format:             pir
end-token:      END SEARCH
--
msu-object:
obj-name:       Enter k-tupel value (word size)
obj-info:       Controls the sensitivity of search. The lower the case the more sensitive
                the search, but also the longer the execution time
obj-tag:        SEARCH KTUP=
obj-class:      Int
min:            1
max:            2
def:            2


###
# EMBL QuickSearch
# 4-Oct-1993
###

service-name:   EMBL QuickSearch server
service-info:   Rapid comparisons of nucleotide sequences, looking for close matches.
service-addr:   quick at EMBL-Heidelberg.DE
--
help-address:   quick at EMBL-Heidelberg.DE
help-body:      help

//

service-nuc-options:
start-token:    SEQ
end-token:      END
maxseqlen:      100000
--
msu-object:
obj-name:       Select sequence library
obj-info:       Subset of database to be searched
obj-tag:        LIB
obj-class:      Group
elements:       2
def:            1
items:          ALL,GENEW
--
msu-object:
obj-name:       Enter window size
obj-info:       Decreasing the window size will increase the sensitivity of the comparison.
                Leave blank if you don't know what you are doing
obj-tag:        WINDOW
obj-class:      Int
min:            1
max:            50
--
msu-object:
obj-name:       Enter stringency
obj-info:       Decreasing the window size will increase the sensitivity of the comparison.
                Leave blank if you don't know what you are doing
obj-tag:        STRINGENCY
obj-class:      Int
min:            1
max:            50
--
msu-object:
obj-name:       Set Perfect flag
obj-info:       Only perfect matches will be found
obj-tag:        PERFECT
obj-class:      Boolean
def:            no
--
msu-object:
obj-name:       Enter minimum percentage of matches
obj-info:       Only hits with overlaps of more than n% identity will be presented
obj-tag:        MATCH
obj-class:      Int
min:            0
max:            100
def:            90
--
msu-object:
obj-name:       Use local homology alignment
obj-info:       If set to yes, a local homology algorithm will be used.
                By default, a Needleman-Wunsch alignment is created
obj-tag:        BEST
obj-class:      Boolean
def:            no
-- 
msu-object:
obj-name:       Search one strand only
obj-info:       Search one strand only. By default, both strands will be searched
obj-tag:        ONE
obj-class:      Boolean
def:            no
--
msu-object:
obj-name:       Enter title of sequence
obj-info:       Short description of the sequence. Will be used as the Subject line
                of the reply
obj-tag:        TITLE
obj-class:      String
maxlen:         70
// no prot options


###
# CBRG (ETH Zuerich)
###

service-name:   CBRG (ETH Zuerich)
service-info:   Exhaustive search of SWISS-PROT protein sequence database
service-addr:   cbrg at inf.ethz.ch
--
help-address:   cbrg at inf.ethz.ch
help-subject:   help
help-body:      help

//

service-nuc-options:
start-token:    NuclPepSearch
lowercase:              no
--
service-prot-options:
start-token:    PepPepSearch
lowercase:              no


###
# BLOCKS server
# 4-Oct-1993
###

service-name:   BLOCKS server    
service-info:   Comparison of protein or DNA sequences against database of protein blocks
service-addr:   blocks at howard.fhcrc.org
--
help-address:   blocks at howard.fhcrc.org
help-body:      help

//

service-prot-options:
seq-format:     fasta
//
service-nuc-options:
seq-format:     fasta


###
# Mail-PROSITE
# 26-Apr-1994
###

service-name:   EMBL PROSITE server
service-info:   Pattern searches using PROSITE database
service-addr:   prosite at embl-heidelberg.de
--
help-address:   prosite at embl-heidelberg.de
help-body:      help

//

service-prot-options:
start-token:    SEQ
seq-format:     ascii
end-token:      END
--
msu-object:
obj-name:       Enter search title
obj-info:       This string will be used as the Subject of the return mail
obj-tag:        TITLE
obj-class:      String
maxlen:         60
---
msu-object:
obj-name:       Include abundant patterns in search
obj-info:       Include abundant patterns. By default, they are excluded.
obj-tag:        FULL
obj-class:      Boolean
def:            no
// no nuc options


###
# MotifFinder
###

service-name:   MotifFinder
service-info:   Motif finding tool at genome.ad.jp
service-addr:   motif at genome.ad.jp
--
help-address:   motif at genome.ad.jp
help-body:      help

//

service-prot-options:
seq-format:     fasta
--
msu-object:
obj-name:       Select motif library
obj-info:       The motif library to be searched
obj-tag:        DATALIB
obj-class:      group
elements:       2
def:            1
items:          Prosite,MotifDic
// no nuc options


###
# ProteinPredict
# 4-Oct-1993
###

service-name:   ProteinPredict
service-info:   Neural network secondary protein structure prediction
service-addr:   PredictProtein at embl-heidelberg.de
--
help-address:   PredictProtein at embl-heidelberg.de
help-subject:   help

//

service-prot-options:
--
msu-object:
obj-name:       Your name
obj-info:       Enter your full name here
obj-tag:        name:
obj-mandatory:  y
obj-class:      string
maxlen:         60
--
msu-object:
obj-name:       Your address (part1)
obj-info:       Enter your postal address here
obj-tag:        address1:
obj-mandatory:  y
obj-class:      string
maxlen:         60
--
msu-object:
obj-name:       Your address (part2)
obj-info:       Enter your postal address here
obj-tag:        address2:
obj-mandatory:  n
obj-class:      string
maxlen:         60
--
msu-object:
obj-name:       Your email address
obj-info:       Enter your email address here
obj-tag:        email:
obj-mandatory:  y
obj-class:      string
maxlen:         60
--
msu-object:
obj-name:       Enter sequence description
obj-info:       A brief description of the sequence
obj-tag:        #
obj-mandatory:  y
obj-class:      string
maxlen:         78
// no nuc options


###
# nnpredict
# 4-Oct-1993
###

service-name:   nnpredict
service-info:   Neural network secondary protein structure prediction
service-addr:   nnpredict at celeste.ucsf.edu
--
help-address:   nnpredict at celeste.ucsf.edu
help-subject:   help
help-body:      help

//

service-prot-options:
lowercase:      n
seq-format:     fasta
--
msu-object:
obj-name:       Select prediction options
obj-info:       nnpredict uses the secondary structure class for prediction:
                (n)   use no tertiary structure class for prediction (the default)
                (a)   use all-alpha tertiary structure class for prediction
                (b)   use all-beta tertiary structure class for prediction
                (a/b) use alpha/beta tertiary structure class for prediction
obj-tag:        option:
obj-class:      Group
elements:       4
def:            1
items:          n,a,b,a/b
// no nuc options


###
# NetGene
# 4-Oct-1993
###

service-name:   NetGene
service-info:   Neural network prediction of splice sites in vertebrates
service-addr:   netgene at virus.fki.dth.dk
--
help-address:   netgene at virus.fki.dth.dk
help-subject:   help
help-body:      help

//

service-nuc-options:
seq-format:     fasta
minseqlen:      451
maxseqlen:      100000
// no prot options

###
# Grail
# 4-Oct-1993
###

service-name:   Grail
service-info:   Gene finding service. Registration required at grail at ornl.gov
service-addr:   grail at ornl.gov
--
help-address:   grail at ornl.gov
help-body:      help
--
reg-address:    grail at ornl.gov
reg-subject:    Registration
reg-options:
msu-object:
obj-name:       Your name
obj-tag:        Name:
obj-mandatory:  y
obj-class:      String
msu-object:
obj-name:       Your affiliation
obj-tag:        Affiliation:
obj-mandatory:  y
obj-class:      String
msu-object:
obj-name:       Your postal address
obj-tag:        Address:
obj-mandatory:  y
obj-class:      String
msu-object:
obj-name:       Your email address
obj-tag:        Email:
obj-mandatory:  y
obj-class:      String
msu-object:
obj-name:       Your phone number
obj-tag:        Phone:
obj-mandatory:  y
obj-class:      String

//

service-nuc-options:
seq-format:     fasta
minseqlen:      100
maxseqlen:      100000
--
msu-object:
obj-name:       Your GRAIL user ID
obj-info:       Enter the user id you received when registering with GRAIL
obj-tag:        Sequences 1
obj-class:      String
// no prot options

###
# GeneID
# 4-Oct-1993
###

service-name:   GeneID (less than 20kb)
service-info:   Pediction of exons and gene structure.
service-addr:   geneid at darwin.bu.edu
--
help-address:   geneid at darwin.bu.edu
help-body:      help

//

service-nuc-options:
start-token:    Genomic Sequences
seq-format:     fasta
minseqlen:      100
maxseqlen:      20000
--
msu-object:
obj-name:       Suppress automatic comparison of best model with protein database
obj-info:       The top-ranking model will NOT be submitted to NCBI's BLAST server
obj-tag:        Genomic Sequence -noblast
obj-class:      Boolean
def:                    no
// no prot options

###
# GenMark
# 4-Oct-1993
###

service-name:   GenMark
service-info:   Gene finding service. Registration required at genmark at ford.gatech.edu
service-addr:   genmark at ford.gatech.edu
service-subject: genmark
--
help-address:   genmark at ford.gatech.edu
help-subject:   instructions
--
reg-address:    genmark at ford.gatech.edu
reg-subject:    Registration
reg-options:
msu-object:
obj-name:       Your name
obj-tag:        Name:
obj-mandatory:  y
obj-class:      String
msu-object:
obj-name:       Your affiliation
obj-tag:        Affiliation:
obj-mandatory:  y
obj-class:      String
msu-object:
obj-name:       Your postal address
obj-tag:        Address:
obj-mandatory:  y
obj-class:      String
msu-object:
obj-name:       Your email address
obj-tag:        Email:
obj-mandatory:  y
obj-class:      String
msu-object:
obj-name:       Your phone number
obj-tag:        Phone:
obj-mandatory:  y
obj-class:      String

//

service-nuc-options:
start-token:    data
--
msu-object:
obj-name:       Select species matrix 
obj-info:       Matrix used to analyze submitted sequence
obj-tag:        SPECIES
obj-class:      Group
elements:       4
def:            1
items:          ecoli, hiexpress,ecophage, human
--
msu-object:
obj-name:       Enter title of analysis 
obj-info:       Short description of the sequence. Will be used as identifier in the reply.
obj-tag:        TITLE
obj-class:      String
--
msu-object:
obj-name:       Select graphical output (PostScript file) 
obj-info:       Will deliver results in the form of a Postscript File
obj-tag:        PSGRAPH
obj-class:      Boolean
def:            n
--
msu-object:
obj-name:       Return CDS predictions with regions 
obj-info:       GenMark replies with a list of regions containing possible coding regions
                from stop codon to stop codon
obj-tag:        PROTEIN region
obj-class:      Boolean
def:            n
--
msu-object:
obj-name:       Return CDS predictions with ORFs 
obj-info:       GenMark replies with a list of open reading frames (splice site to splice 
                site)
obj-tag:        PROTEIN orf
obj-class:      Boolean
def:            n
--
msu-object:
obj-name:       Send predicted ORFs automatically to BLAST server 
obj-info:       ORFs in which coding regions are predicted are automatically submitted to
                NCBI's BLAST server for homology searches
obj-tag:        PROTEIN send
obj-class:      Boolean
def:            n
--
msu-object:
obj-name:       Send nucleotide sequences of predicted ORFs automatically to BLAST server
obj-info:       Nucleotide sequences of ORFs in which coding regions are predicted are
                automatically submitted to NCBI's BLAST server for homology searches
obj-tag:        NUCSEQ send
obj-class:      Boolean
def:            n
--
msu-object:
obj-name:       Select ORF list display format 
obj-info:       orf gives detailed assessment of regions between splice-sites that are
                      predicted to contain coding regions;
                region cites regions from stop codon to stop codon in which a coding region
                      was predicted;
                off tells GenMark not to reply with an ORF list
obj-tag:        ORFLIST
obj-class:      Group
elements:       3
def:            1
items:          orf, region, off
--
msu-object:
obj-name:       Enter alternative email address 
obj-info:       Fill in if GenMark should use alternative email address
obj-tag:        ADDRESS
obj-class:      String
--
msu-object:
obj-name:       Enter user name 
obj-info:       You may fill in your name here for identification purposes
obj-tag:        NAME
obj-class:      String
--
msu-object:
obj-name:       Enter Markov chain order 
obj-info:       Specifies the order of the Markov chain used to analyze the sequence.
                Should be unnecessary to specify
obj-tag:        ORDER
obj-class:      Int
/* Don't know whether these values have any resemblance to reality */
min:            1
max:            10
--
msu-object:
obj-name:       Enter window size 
obj-info:       Length of the analysis window that the GenMark algorithm uses. Smaller values
                will produce a higher rate of false signals, but may show smaller coding
                regions. Larger values will clarify the signal of larger regions but yield
                lower sensitivity. Should be unnecessary to modify
obj-tag:        WINDOW
obj-class:      Int
min:            1
max:            100000
def:            96
--
msu-object:
obj-name:       Enter window step size 
obj-info:       Step size that the GenMark algorithm uses to advance the window. Smaller values
                increase the resolution of a graph and increases the output size. 
                Should be unnecessary to modify
obj-tag:        STEP
obj-class:      Int
min:            1
max:            100000
def:            12
--
msu-object:
obj-name:       Enter prediction threshold 
obj-info:       This threshold will be used to judge whether a region should be predicted as
                coding
obj-tag:        THRESHOLD
obj-class:      Float
min:            0
max:            1
def:            0.6
// no prot options

###
# Pythia
# 4-Oct-1993
###

service-name:   PYTHIA (Rpts)
service-info:   Identification of occurrences of repetitive DNA elements
service-addr:   pythia at anl.gov
service-subject: Rpts
--
help-address:   pythia at anl.gov
help-subject:   help

//

service-nuc-options:
seq-format:     ig
maxseqlen:      10000
lowercase:      no

//

service-name:   PYTHIA (Alu)
service-info:   Identification of subfamily membership of Alu sequences
service-addr:   pythia at anl.gov
service-subject: Alu
--
help-address:   pythia at anl.gov
help-subject:   help

//

service-nuc-options:
seq-format:     ig
maxseqlen:      10000
lowercase:      no


###
# GenomeNet BLAST
# 5-Oct-1993
###

service-name:   GenomeNet BLAST
service-info:   BLAST similarity searches on the Japanese GenomeNet server 
service-addr:   blast at genome.ad.jp
--
help-address:   blast at genome.ad.jp
help-body:      help

//

service-nuc-options:
start-token:    BEGIN
seq-format:     fasta
--
msu-object:
obj-name:       Select program to use
obj-info:       blastn is nucleotide seq vs. nucleotide db,
                blastx is translated nucleotide seq vs. protein db
obj-tag:        PROGRAM
obj-mandatory:  y
obj-class:      Group
elements:       2
def:            1
items:          blastn,blastx
--
msu-object:
obj-name:       Select database
obj-info:       Subset of database to be searched
obj-tag:        DATALIB
obj-mandatory:  y
obj-class:      Group
elements:       7
def:            1
items:          nr-nt, genbank, embl,nr-aa, swissprot, pir,prf
--
msu-object:
obj-name:       Enter number of scores
obj-info:       Number of scores to report
obj-tag:        V=
obj-class:      Int
min:            1
max:            1000
def:            500
--
msu-object:
obj-name:       Enter number of high-scoring segment pairs
obj-info:       Number of high-scoring segment pairs to report
obj-tag:        B=
obj-class:      Int
min:            1
max:            1000
def:            250
--
msu-object:
obj-name:       Enter score for matches
obj-info:       The score to assign to a single-letter match
obj-tag:        M=
obj-class:      Int
min:            1
max:            1000
def:            5
--
msu-object:
obj-name:       Enter score for mismatches
obj-info:       The score to assign to a single-letter mismatch
obj-tag:        N=
obj-class:      Int
min:            -1000
max:            -1
def:            -4
//
service-prot-options:
start-token:    BEGIN
seq-format:     fasta
--
msu-object:
obj-name:       Select program to use
obj-info:       blastp is protein seq vs. protein,
                tblastn is protein seq vs. translated nucleotide db
obj-tag:        PROGRAM
obj-class:      Group
elements:       2
def:            1
items:          blastp,tblastn
--
msu-object:
obj-name:       Select database
obj-info:       Subset of database to be searched
obj-tag:        DATALIB
obj-mandatory:  y
obj-class:      Group
elements:       7
def:            1
items:          nr-aa, swissprot,pir,prf,pdbstr, nr-nt, genbank,embl
--
msu-object:
obj-name:       Enter number of scores
obj-info:       Maximum number of scores to report
obj-tag:        V=
obj-class:      Int
min:            1
max:            1000
def:            500
--
msu-object:
obj-name:       Enter number of high-scoring segment pairs
obj-info:       Maximum number of high-scoring segment pairs to report
obj-tag:        B=
obj-class:      Int
min:            1
max:            1000
def:            250


###
# GenomeNet FASTA
# 5-Oct-1993
###

service-name:   GenomeNet FASTA
service-info:   FASTA similarity searches on the Japanese GenomeNet server 
service-addr:   fasta at genome.ad.jp
--
help-address:   fasta at genome.ad.jp
help-body:      help

//

service-nuc-options:
start-token:    BEGIN
seq-format:     fasta
--
msu-object:
obj-name:       Select database
obj-info:       Subset of database to be searched
obj-tag:        DATALIB
obj-mandatory:  y
obj-class:      Group
elements:       30
def:            1
items:          nr-nt, genbank,genbank-upd, genbank/primate,genbank/rodent,
                genbank/other_mammalian,genbank/other_vertebrate,genbank/invertebrate,
                genbank/plant,genbank/bacterial,genbank/structural_rna,
                genbank/viral,genbank/phage,genbank/synthetic,genbank/unannotated,
                genbank/est,genbank/patent, embl,embl/bacteriophage,embl/fungi,
                embl/invertebrate,embl/organelle,embl/other_mammalian,
                embl/other_vertebrate,embl/plant,embl/primate,embl/prokaryote,
                embl/rodent,embl/synthetic,embl/unannotated,embl/viral
--
msu-object:
obj-name:       Enter k-tupel value (word size)
obj-info:       Controls the sensitivity of search. The lower the case the more sensitive
                the search, but also the longer the execution time
obj-tag:        KTUP
obj-class:      Int
min:            3
max:            6
def:            6
--
msu-object:
obj-name:       Enter number of scores
obj-info:       Number of scores to report
obj-tag:        -b
obj-class:      Int
min:            1
max:            100
def:            50
--
msu-object:
obj-name:       Enter number of best alignments
obj-info:       Number of alignments to report
obj-tag:        -d
obj-class:      Int
min:            1
max:            100
def:            10
//
service-prot-options:
start-token:    BEGIN
seq-format:     fasta
--
msu-object:
obj-name:       Select program to use
obj-info:       FASTA is protein seq vs. protein db,
                TFASTA is protein seq vs. translated nucleotide db
obj-tag:        PROGRAM
obj-class:      Group
elements:       2
def:            1
items:          fasta,tfasta
--
msu-object:
obj-name:       Select database
obj-info:       Subset of database to be searched
obj-tag:        DATALIB
obj-mandatory:  y
obj-class:      Group
elements:       35
def:            1
items:          nr-aa, swissprot,pir,prf,pdbstr,
                nr-nt, genbank,genbank-upd, genbank/primate,genbank/rodent,
                genbank/other_mammalian,genbank/other_vertebrate,genbank/invertebrate,
                genbank/plant,genbank/bacterial,genbank/structural_rna,
                genbank/viral,genbank/phage,genbank/synthetic,genbank/unannotated,
                genbank/est,genbank/patent, embl,embl/bacteriophage,embl/fungi,
                embl/invertebrate,embl/organelle,embl/other_mammalian,
                embl/other_vertebrate,embl/plant,embl/primate,embl/prokaryote,
                embl/rodent,embl/synthetic,embl/unannotated,embl/viral
--
msu-object:
obj-name:       Enter k-tupel value (word size)
obj-info:       Controls the sensitivity of search. The lower the case the more sensitive
                the search, but also the longer the execution time
obj-tag:        KTUP
obj-class:      Int
min:            1
max:            2
def:            2
--
msu-object:
obj-name:       Enter number of scores
obj-info:       Number of scores to report
obj-tag:        -b
obj-class:      Int
min:            1
max:            100
def:            50
--
msu-object:
obj-name:       Enter number of best alignments
obj-info:       Number of alignments to report
obj-tag:        -d
obj-class:      Int
min:            1
max:            100
def:            10




###
# GenQuest (Q)
# 1-Nov-1993
###

service-name:   GenQuest (Q)
service-info:   Database searches
service-addr:   q at ornl.gov
--
help-address:   q at ornl.gov
help-body:      help

//

service-nuc-options:
start-token:    SEQ
end-token:      END
seq-format:     ascii
--
msu-object:
obj-name:       Sequence type
obj-tag:        TYPE DNA
obj-mandatory:  y
obj-class:      Fixed
--
msu-object:
obj-name:       Select database
obj-info:       Database to be searched
obj-tag:        TARGET
obj-class:      Group
elements:       2
def:            1
items:          GSDB, Repetitive
--
msu-object:
obj-name:       Select search method
obj-info:       Search method to be used (SW = Smith-Waterman)
obj-tag:        METHOD
obj-class:      Group
elements:       4
def:            1
items:          SW, FASTA, BLAST, FLASH
--
msu-object:
obj-name:       Apply filter for repetitive sequences
obj-info:       Removes repetitive elements from query sequence
obj-tag:        FILTER
obj-class:      Boolean
def:            y
--
msu-object:
obj-name:       Enter comment
obj-info:       To tag your sequence with some identifier
obj-tag:        COMMENT
obj-class:      String
--
msu-object:
obj-name:       Enter number of scores (only for SW searches)
obj-info:       Number of scores to report
obj-tag:        SCORE
obj-class:      Int
min:            1
max:            1000
def:            10
--
msu-object:
obj-name:       Enter number of alignments (only for SW searches)
obj-info:       Number of alignments to report
obj-tag:        ALIGN
obj-class:      Int
min:            1
max:            1000
def:            10
//
service-prot-options:
start-token:    SEQ
end-token:      END
seq-format:     ascii
--
msu-object:
obj-name:       Sequence type
obj-tag:        TYPE PROTEIN
obj-mandatory:  y
obj-class:      Fixed
--
msu-object:
obj-name:       Select database
obj-info:       Database to be searched
obj-tag:        TARGET
obj-class:      Group
elements:       3
def:            1
items:          SWISSPROT, PDB, PROSITE
--
msu-object:
obj-name:       Select search method
obj-info:       Search method to be used (SW = Smith-Waterman)
obj-tag:        METHOD
obj-class:      Group
elements:       4
def:            1
items:          SW, FASTA, BLAST, FLASH
--
msu-object:
obj-name:       Scoring matrix
obj-info:       Scoring matrix applied for sequence comparisons
obj-tag:        MATRIX
obj-class:      Group
elements:       5
def:            1
items:          BLOSUM60, BLOSUM80, PAM40, PAM120, PAM250
--
msu-object:
obj-name:       Enter comment
obj-info:       To tag your sequence with some identifier
obj-tag:        COMMENT
obj-class:      String
--
msu-object:
obj-name:       Enter number of scores (only for SW searches)
obj-info:       Number of scores to report
obj-tag:        SCORE
obj-class:      Int
min:            1
max:            1000
def:            10
--
msu-object:
obj-name:       Enter number of alignments (only for SW searches)
obj-info:       Number of alignments to report
obj-tag:        ALIGN
obj-class:      Int
min:            1
max:            1000
def:            10

###
# SBASE Mail server
# 10-Dec-1993
###

service-name:   SBASE
service-info:   Protein domain detection
service-addr:   sbase at icgeb.trieste.it
--
help-address:   sbase at icgeb.trieste.it
help-body:      help

//

service-prot-options:
start-token:    BEGIN
seq-format:     FASTA
--
msu-object:
obj-name:       Include annotation
obj-info:       Include complete annotation of domains in output
obj-tag:        ANNOTATIONS
obj-class:      Group
elements:       2
def:            1
items:          YES, NO
--
msu-object:
obj-name:       Scoring matrix
obj-info:       Scoring matrix applied for sequence comparisons
obj-tag:        MATRIX
obj-class:      Group
elements:       5
def:            1
items:          PAM120, PAM250, PAM40, BLOSUM60, BLOSUM80
--
msu-object:
obj-name:       Cutoff score
obj-info:       Cutoff score for displaying homologies
obj-tag:        SCORE PARAMETER
obj-class:      Int
min:            30
max:            100
def:            35

###
# ProDom
# 14-Mar-1994
###

service-name:   ProDom
service-info:   ProDom domain searches
service-addr:   prodom at toulouse.inra.fr
--
help-address:   prodom at toulouse.inra.fr
help-body:      help

//

service-nuc-options:
start-token:    BEGIN
end-token:      END
seq-format:     fasta
--
msu-object:
obj-name:       Search type
obj-tag:        PROGRAM blastx
obj-mandatory:  y
obj-class:      Fixed
//
service-prot-options:
start-token:    BEGIN
end-token:      END
seq-format:     fasta
--
msu-object:
obj-name:       Search type
obj-tag:        PROGRAM blastp
obj-mandatory:  y
obj-class:      Fixed

###
# GCRDb
# 26-Apr-1994
###

service-name:   GCRDb (G-protein coupled receptors)
service-info:   FASTA searches of G-protein-coupled receptor database
service-addr:   gcrdb at receptor.mgh.harvard.edu
--
help-address:   gcrdb at receptor.mgh.harvard.edu
help-body:      help

//

service-prot-options:
seq-format:     fasta
//





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