Mailfasta 3.2, New version

Thon de Boer deboer at bio.vu.nl
Thu Jul 15 07:38:22 EST 1993


I have just posted the most recent version of my program mailfasta to 
bionet.software.sources. It will appear there when it has been approved by the
moderator.

Mailfasta is a UNIX csh program which will take a sequence and send a specially
formatted mail message to the different mailservers, where it will be compared
with databases or processed in other ways.

It can also be obtained from the iubio archive of Dob Gilbert (ftp.bio.indiana.edu)
first from the Incoming directory, but later it will be moved to the molbio/unix
directory.
Mailfasta can also be obtained via my gopher service :

Type=1
Name=Molecular Biology Unix software
Path=1/unix_molbio_software
Host=grampus.bio.vu.nl
Port=9001

Thon de Boer

CHANGES SINCE THE LAST VERSION

Version 3.2 (July 11, 1993)
     * The EMBL FASTA server has returned to this version. It has replaced the
         FASTA server in Japan. The respons time of the server at EMBL in
         Germany is much shorter now and it has a wider range of databases to
         be searched.
     * The BLITZ server at EMBL has been added. 
         This service runs the MPsrch program of Shane Sturrock and John Collins
         Edinburgh, UK.  It performs extrememly fast "best local similarity"
         searches of the Swiss-Prot protein sequence database, using the well
         known Smith and Waterman algorithm.
     * The PDB database has been added to the databases to be searched using
         the BLAST server at NCBI

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.

Version 3.0 (August, 22 1992)
     There have been a lot of changes since the last version of mailfasta (2.1)
     Version 3.0 no longer uses the FASTA and BLAST server at the GenBank site
     (genbank.bio.net) as those services will be terminated soon. Instead it
     uses the FASTA server at the FLAT site in Japan. This site does not have
     the vector subset, so this cannot be searched using the FASTA program.
     Version 3.0 now uses the NCBI site with the BLAST program which can search
     almost all DNA and PROTEIN databases.
     It can also search a query for PROSITE blocks using the BLOCKS server.
     ORF predicting is now possible using the GRAIL and GeneID/NetGene server.
     Retrieving sequence entries is no handled by the NCBI RETRIEVE server.
     Getentry now needs a database name and a LOCUS name from that database to
     be retrieved. A better way to retrieve sequence entries is to use the
     gopher hole at iubio and the EMBNET hole in switserland.




More information about the Bio-soft mailing list