🚀 go-pugleaf

I sent this out a week ago, but due to local distribution problems, most of
the world never saw it.
For the people that did see the previous announcement,
an important new feature is added, so do read on.
Also people looking for non WWW access to the databases could be interested

Included is a short manual on the use of an FTP to SRS gateway, developed
in the EMBL Outstation - EBI. It can be used right now, but I do not 
garantee yet, that the service will be officially supported.
Please try it, and if you find any problems, or have any suggestions, let
me know (jecop@ebi.ac.uk)
The idea is that it can be used in automated checking/retrieving new
sequences of interest.

Jeroen

-
USING SRS (Sequence Retrieval System [1]) from Anonymous FTP
------------------------------------------------------------
(Jeroen Coppieters, 17-Mar-1995, srsftp version 1.1beta)

This document describes SRSFTP as it is maintained at 
EMBL Outstation, the European Bioinformatics Institute
further referenced as "the EBI"

The Anonymous FTP server of the EBI has a gateway to SRS,
developped by Jeroen Coppieters and RJ White.
This allows the retrieval of sequences from Swissprot and EMBL (as well as 
all other databases that are maintained in SRS at the EBI [2]), using
the power of SRS.
A query can be executed from any directory, after connecting to the
anonymous ftp server.

All results of the query will be stored in the file you name.
The sequences are stored in flat-file EMBL format by default

In any query, the * wildcard can be used

three formats of queries are available:
 - simple sequence retrieval
 - simple srs query
 - full srs query

1) SIMPLE SEQUENCE RETRIEVAL
---------------------------
FORMAT: 
get DB:INDEX:QUERYSTRING FILENAME

DB is one of the following:
embl, emblnew, emblall, nuc
swissprot, swissnew, swissall, pep
if any of the xxall databases is specified, both the release and the
updates are searched. If a sequence has been updated since the last
release, both the old and new entry will be returned.

INDEX  DATABASE SEARCHFIELD          QUERYSTRING
acc      accession number            accession nr (e.g. X07888)
id       identifier                  identifier (e.g. ATP6_YEAST)
dat      date                        date (e.g. 20-NOV-1994)
fts      feature                     feature name (e.g. intron)
ref      reference                   Journal reference
                                     (e.g. Plant Mol. Biol. 10:91-104(1987))
sl       sequence length             number (e.g. 2400)
                                     or range (e.g. 2300:5000)
def      definition                  string
aut      author                      string
cc       comment                     string
org      organism                    string
tit      reference title             string
all      all text fields             string

EXAMPLES:
get emblall:acc:x07888 x07888.seq
retrieve sequence from embl/emnew with accession number x07888
store in the file x07888.seq

get swissprot:all:nitrate* nitrate.pep
get all swissprot entries that have a word starting with nitrate
in any of the text fields.
Store in the file nitrate.pep


2) SIMPLE SRS QUERY
------------------
FORMAT:
get srs:QUERYSTRING

This allows linking of several databases

For more information on SRS queries, have a look at the SRS manual
This however does not allow the complete functionality of SRS.
Restrictions are: - NO SPACES are allowed in the query.
                  - no command line parameters can be included

EXAMPLES
get srs:[embl-fts:intron]>parent&[embl-org:arabidopsis*] arain.seq
retrieve all sequences from Arabidopsis spec. that contain an intron.

get srs:[prosite-id:PROTEIN_KINASE_TYR]>swissprot kinase.pep
retrieve all proteins, that contain a tyrosine kinase motif (PROSITE)

get srs:[prosite-id:PROTEIN_KINASE_TYR]>swissprot>pdb kinase.pdb
retrieve 3D structures (if known) from the above proteins

3) FULL SRS QUERY
-----------------
If you want to have access to command line options (e.g. to change the
output format), a full blown getz command is available.

FORMAT:
From UNIX, VMS+Multinet, MSDOS+NCSA ftp:
get getz+commandline+options+querystring filename

VMS+UCX:
get "getz+commandline+options+querystring" filename

- All spaces in the query should be replaced by plus (+)
- If you want to include a + in a query, use a double plus (++)
- do not put quotes round the querystring 
- if you want to escape a character with a backslash (\), duplicate
  the backslash (\\)
- contrary to forms 1 and 2, there is no colon in the command

- the getz program has a new command line option -pipe "string"
  where string can be "/bin/compress" or "/bin/gzip"
  this will compress the results before transmitting the data,
  thus minimizing network traffic
  Do not forget to use BINARY TRANSFER if you use this option

- On UNIX systems, whenever ftp expects a filename,
  this can be replaced by - (dash)
  the retrieved file will be printed on stdout 

EXAMPLES
get getz+-help file
retrieve help on the usage of getz

get getz+-libs libs.lst
get a list of all available databases

get getz+-d+-sf+fasta+-pipe+"/bin/gzip"+[emnew-org:drosophila*] dro.seq.gz
retrieve all Drosophila sp. sequences from emnew in fasta format. Gzip
before transmitting

get getz+-l+swissprot+-l+swissnew+[sq-id:*_ecoli] ecoli.lst
generate a list of all ecoli proteins in swissprot and swissnew

============================================================
NOTES:
-----
[1] More information on SRS is available from the author: Thure Etzold
Via WWW: http://www.embl-heidelberg.de/srs/srsman.html

Refererences:
Thure Etzold and Patrick Argos, SRS an indexing and retrieval tool for flat 
file data libraries. Comput. Appl. Biosci. 9:49-57, 1993 

Thure Etzold and Patrick Argos, Transforming a set of biological flat file 
libraries to a fast access network. Appl. Biosci. 9:59-64, 1993 

[2] on March 14th 1995, these database were:
                 Library   Group              Entries    Index Date
-------------------------------------------------------------------
               SWISSPROT   Sequence             40292       2/28/95
                SWISSNEW   Sequence              9036        3/8/95
                     PIR   Sequence             71995       2/28/95
                    EMBL   Sequence            234501       2/28/95
                   EMNEW   Sequence            102576       3/14/95
                   NRL3D   Sequence              4153        3/1/95
                   NRSUB   Sequence               248        3/1/95
                     PDB   ProteinStruct         3391        3/1/95
                    HSSP   ProteinStruct         3070        3/4/95
                    DSSP   ProteinStruct         2968        3/2/95
                     ALI   ProteinStruct           84        3/1/95
                    FSSP   ProteinStruct          436        3/4/95
                 PROSITE   SeqRelated            1029        3/1/95
              PROSITEDOC   SeqRelated             786        3/1/95
                  BLOCKS   SeqRelated             770        3/1/95
                     EPD   SeqRelated            1251        3/1/95
                    ECDC   SeqRelated            3571        3/1/95
                  ENZYME   SeqRelated            3546        3/1/95
                  REBASE   SeqRelated            2454        3/1/95
                  PRODOM   SeqRelated           23105        3/1/95
                 FLYGENE   SeqRelated            7126       3/10/95
                SWISSDOM   SeqRelated           28224        3/1/95
                  PIRALN   SeqRelated            1183        3/1/95
              SEQANALREF   Literature            2579        3/1/95
                 MEDLINE   Literature          179262        3/1/95
                    LIMB   Others                 120        3/1/95
                  TFSITE   TransFac              4042       3/14/95
                TFFACTOR   TransFac              1412       3/14/95
                   DBEST   TaggedSites           3264        3/8/95


--
======================================================================
         . O .                               Jeroen Coppieters
     . O O o   O .                            Software Support
   O O O O *o    O O          Jeroen.Coppieters@embl-ebi.ac.uk
  O O O O(   *o  )O O                     (or jecop@ebi.ac.uk)
  )O O O O   o*  O O(                         ++44 1223 494422 
  O O O O( o*    )O O
  )O O O O  *o   O O(                      EMBL Outstation EBI
  O O O O(   *o  )O O      (European Bioinformatics Institute)
  )O @ O O   o*  O O(                             Hinxton Hall
    O O O( o*   )O('                                   Hinxton
     ` O(   *o O  '                         Cambridge CB10 1RQ
         ` O '                                              UK
http://www.ebi.ac.uk
======================================================================