MOTIF E-Mail Server on GenomeNet
A set of motif libraries and search programs is being organized at the
Supercomputer Laboratory, the Institute for Chemical Research, Kyoto
University for retrieval and analysis of protein sequence and structural
motifs. The program currently available is:
MotifFinder
written by Atsushi Ogiwara (unpublished)
and the motif libraries on service are:
Prosite
A. Bairoch, "PROSITE: A dictionary of sites and patterns in proteins"
Nucleic Acids Res. 20, 2013-2018 (1992)
MotifDic
A. Ogiwara, I. Uchiyama, Y. Seto, and M. Kanehisa, "Construction of
a dictionary of sequence motifs that characterize groups of related
proteins", Protein Eng. 5, 479-488 (1992)
Accessing the MOTIF server
To access the server, send an electronic mail message containing the
formatted query sequence (as described below) to the following Internet
address:
motif@genome.ad.jp
Obtaining Help
If you would like to receive instructions on using the MOTIF server,
send a mail message to the address above containing the word "help" on
a single line. This document is then returned to you in a mail message.
About MotifFinder
MotifFinder is designed to help understand biological meaning of your
query sequence. It first searches a library of sequence motifs for
patterns that appear in your query sequence. If any patterns are found
MotifFinder then searches both protein sequence (Swiss-Prot or PIR1)
and structural (PDB) databases for those sequences and structures that
contain the patterns. The result is given in graphical representations
using PostScript codes, where you can view the location of the pattern
on the 3-D structure and in relation to known biological function sites
annotated in the sequence databases.
Sending the Query Sequence
To search for motifs in your sequence, send your sequence in FASTA
format like:
>my_query this is my query sequence
MNVAINGFGRIGRLVLRASAKNPLINIVAINDPFVSTTYMEYMLEYDTVHGKFDGSLSHD
ETHIFVNGKPIRVFNEMNPENIKWGEEQVQYVVESTGAFTTLEKASTHLKNGVEKVVISA
PSSDAPMFVMGVNHELYEKNMHVVSNASCTTNCLAPLAKVVNDKFGIKEGLMTTVHAVTA
TQKTVDGPSKKDWRGGRGACFNIIPSSTGAAKAVGKVIPSLNGKLTGMSFRVPTADVSVV
DLTARLVNPASYDEIKAAIKSASENEMKGILGYTEKAVVSSDFIGDSHSSIFDAEAGIAL
TDDFVKLVSWYDNEWGYSSRVLDLIEHMVKNE
The first line must begin with a greater-than sign ">" followed by the
name of the sequence and an optional note about the sequence. The
sequence data begin on the next line without the greater-than sign.
The default motif library to be searched is Prosite, but this may
be changed by the DATALIB parameter which should be included before
the sequence data as follows:
DATALIB MotifDic
>my_query ...
......
Use your local mail program to send your query sequence. Most mail
programs allow you to import a file containing your sequence into
the mail message.
Interpreting the Result
If MotifFinder finds any sequence motifs in your query sequence, it
returns the information about the motif and the location on your
sequence. In addition, the mail reply contains, at most, two more
sections of PostScript codes which may be used to help interpret
biological meaning of your sequence.
To facilitate the extraction of the three sections, the mail reply
is encoded in a shell script. You should follow the procedure below:
1. Save the mail reply into a file.
2. Edit the file and remove the mail header section at the beginning.
3. Apply "csh" command to this file.
This will create files named
MotifFind.0, MotifFind.1, ... for the location of motifs
MotifFeat0.ps, MotifFeat1.ps, ... for feature representation
Motif3D0.ps, Motif3D1.ps, ... for 3-D representation
where the numerals 0,1,... distinguish different motifs found.
The first set of files are text files, but the second and third sets
are PostScript files. You may display them with a PostScript viewer
such as PageView in Sun OpenWindows, or print them out to a PostScript
printer such as Apple LaserWriter or Sun SPARCprinter.
The MotifFeat file contains a schematic diagram of the primary
structures showing both the locations of motifs and the locations of
functional sites annotated in the database. In this diagram boxes
correspond to motifs, arrows and triangles mean active/binding sites
and intron positions, respectively, as annotated in the feature table
of the database.
The Motif3D file, if it exists, is a graphical representation of
structural entries in the PDB database. It is a stereo drawing of
alpha-carbon tracing with the locations of motifs in the three-dimensional
structure marked in bold lines.
We Ask Your Comments
We welcome your comments and suggestions to make the MOTIF server
a more valuable resource to the biological community. The address
is: Motif-Manager@genome.ad.jp.
Last Update: 93/03/16
==========================================================================
________________________________________