Mailfasta 3.1 uploaded

Thon de Boer deboer at bio.vu.nl
Fri Feb 19 17:50:25 EST 1993


There is a new version of my program mailfasta. The most recent version is 3.1
It contains some new databases and servers (2D structure predicting)
It can be found on the iubio archive site (iubio.bio.indiana.edu). 
First in the incoming directory and later in molbio/unix (if all goes well).
It can also be found on the EMBL archive site (embl-heidelberg.de).
This is the README file :

*****
This is version 3.1 of the mailfasta program. It is a UNIX shell script which
will take a DNA or PROTEIN sequence and will mail it to all the
different mail-servers where it can be searched against the DNA or PROTEIN
databases using the FASTA and/or BLAST programs. It can also be used to identify
ORFs using the GRAIL and/or GeneID/NetGene mail servers and to identify homology
using PROSITE blocks with the BLOCKS server.
A new server is added which can give multiple alignments and some info on
the secondary structure.
It uses the new BLAST server at NCBI and the FLAT server in Japan for FASTA
searches because the services at GenBank will be terminated at the end of this
month. 

It is packed as an shell archive. It contains :
mailfasta : the UNIX shell script
cid.c     : A small c program which will determine if the sequence is DNA or AA
getentry  : A shell script which can be used to retrieve entries of interest
mailfasta.doc : The documentation file
mailfasta.changes : A file stating the changes since version 2.1

The shar file will unpack all these files and will compile cid.c into cid
using the cc c compiler.

mailfasta makes use oif the program 'readseq' for file conversion.
This program MUST be present and is NOT packed with this shar file.
It can be obtained via FTP from various FTP sites (fly.bio.indiana.edu etc.)

This shar file can also be found on this FTP site. First in the 'incomming'
directory and later in the /molbio/unix directory.

CHANGES SINCE THE LAST VERSION

Version 3.1 (February 18, 1993)
     * Two new servers have been added :
         Pythia (Human repetitive DNA and ALU subfamily membership)
         Predict 2D structure of a AA sequence
     * Three new databases have been added to the BLAST search :
         Alu (Human repetitive elements)
         Kabat (Sequences of immunological interest)
         Swiss-Prot Update (Cumulative weekly update)
     * Option -d has been added. If option -d is used, mailfasta operates in
     the default mode. After -d one number and one sequenfile can be given.
     The number is the number of the service to be used for the sequence file.
     The sequence will be emailed to the requested service with the default
     settings for that service. If there are no errors mailfasta will return
     no messages.
     The '-d sequencfile' part can be repeated several times. It is also
     posible to give a sequencfilename after the '-d # file' part for normal
     interactive mode. So :

        mailfasta -d 18 file1 -d 1 file2 file3 file4 -d 13 file5

     is possible.

Sincerely,
Thon de Boer




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