FreeBSD Manual Pages

home | help

exonerate-server(1) sequence comparison server exonerate-server(1)

NAME
exonerate-server - a sequence comparison server for exonerate

SYNOPSIS
exonerate-server [ options ] <index path>

DESCRIPTION
exonerate-server is a multi-threaded server for the exonerate sequence
alignment program.

It uses a set of sequences and a corresponding index file to allow fast of
large datasets.

OVERVIEW
Firstly, an .esd file must be made from the sequence files. The .esd file
is an Exonerate Sequence Dataset file, and can be used to group together
any set of sequences where each sequences containing unique identifiers.
This is done by using the fasta2esd utility.

fasta2esd genome.fasta genome.esd

Next, an .esi file my be made from the .esd file. The .esi file is an Ex-
onerate Sequence Index file, and contains an index or set of indices corre-
sponding to a particular dataset. This is done by using the esd2esi util-
ity.

esd2esi genome.esd genome.esi

Once the .esi file has been generated, the exonerate-server may be started.

exonerate-server genome.esi

While the server is running, exonerate may be used to query the server by
replacing the target sequences in the command line with the name of the
server and port number. The default port number for the exonerate-server
is 12886.

exonerate query.fasta localhost:12886

OPTIONS
Some of the command line options for the exonerate-server are the same as
for the exonerate client, and these are documented in the man page for ex-
onerate. The other options which are specific to exonerate-server are doc-
umented here.

--port <port>
Specify the port on which the server should listen. By default, ex-
onerate-server will listen on port 12886, but alternative ports may
be specified with this option.

--input <index file>
Specify the index file to be used when the server is started. This
option is mandatory. The index file is a .esi file generated by the
esd2esi utility.

--preload <boolean>
By default the indices contained in the .esi file, and the sequences
referenced in the corresponding .esd file are loaded into memory
when the server is started. This is necessary to achieve fast per-
formance that would otherwise be hampered by frequent disk accesses.
This option allows the index and sequence preloading to be turned
off, which allows the server to run much more slowly, but with
faster startup and a smaller memory footprint. It is not advised to
turn preloading off unless testing or debugging the server.

--maxconnections <count>
The server is multithreaded. This option sets the number client
processes which are allowed to connect to the server simultaneously.
For good performance, it should not be set to more than the number
of CPUs on the machine on which the server is running.

--verbosity <level>
Set the verbosity level for the server. If it is zero, the server
will be silent, and the higher the number, the more messages are re-
ported by the server about what is happening.

INTERFACE
This section documents the communication interface between the client and
server. The interface is documented for people wishing to write their own
custom server to sit behind exonerate - for normal use of exonerate, it is
not necessary to know this.

The interface works by the client sending simple command lines and the
server sending simple reply lines over a socket. All the commands and
replies are simple lines of ASCII text, so it is possible to use telnet as
a client for testing a server.

Any command is a single line of text, but a reply may contain many lines of
text. The replies are in the form of <tag>: <message>

Any reply can include lines with the tag warning: or error: These warning:
and error: tags are echoed by the client, and the client will exit after
receiving any error: reply.

When the server is returning a multiline reply, the first line must show
the number of lines in the whole reply as: linecount: <count> For examples,
see the replies from the get hsps commands in the example session below.

The client will only open a single connection to any server, although a
multithreaded server is obviously required to allow multiple clients to
connect simultaneously.

Commands and replies used in for the interface.
Command: version
Reply: version <server name> <server version>

Command: exit
Reply: ( no reply - server closes connection )

Command: dbinfo
Reply: dbinfo: <type> <masked> <num_seqs> <max_seq_len> <total_seq_len>

The dbinfo command returns information about the database loaded
on the server. The returned fields are:

<type> either dna or protein
<masked> either softmasked or unmasked
<num_seqs> the number of sequences in the database
<max_seq_len> the length of the longest sequence in the data-
base
<total_seq_len>
the total length of all the sequences in the
database

Command: lookup <eid>
Reply: lookup: <iid>

The lookup command is used to map an external identifier to an
internal identifier.

Command: get info <iid>
Reply: seqinfo: <len> <checksum> <eid> [ <def> ]

The get info command returns information about a sequence in the
database. The returned fields are:

<len> the sequence length
<checksum> a gcg format checksum (see below)
<eid> the external id (eg. from fasta header)
<def> a description line for the sequence (also from
the fasta header), this field is optional an may
be ommitted.

Command: get seq <iid>
Reply: seq: <seq>

The get seq command returns a whole sequence on one line.

Command: get subseq <iid> <start> <len>
Reply: subseq: <sequence>

The get subseq command returns part of a sequence. The start of
the sequence is position zero. eg. get subseq 0 0 10 will return
the first 10 bases of the first sequence in the database.

Command: set query <seq>
Reply: ok: <len> <checksum>

The seq query command is used to send a query sequence to the
server. It returns the length of the sequence and a gcg checksum

Command: revcomp <query | target>
Reply: ok: <query | target> strand <forward | revcomp>

The revcomp query command makes the server reverse complement the
query. This is to save the bandwidth of sending the query twice.

The revcomp target command is to tell the server to treat the
database as its reverse complement. The client only sends this
command when searching a translated database, so need not be im-
plemented for most types of search.

Command: set param <name> <value>
Reply: ok: <set | ignored>

The set parameter command sends parameters from the exonerate
command line to the server. This commands can all be ignored by
the client for a basic implementation, but cannot be ignored for
optimal performance.

Command: get hsps
Reply: hspset: <iid> { <query_pos> <target_pos> <length> }
Or: hspset: empty

The get hsps command is the main command for getting sets of
hsps. The server may return multiple hspsets. The returned
fields are:

<iid> The internal id of the target sequence for these
HSPsets.
<query_pos> The hsp query start position
<target_pos> The hsp target start position
<length> The hsp length

The last three fields represent an HSP, and may be repeated many
times on one hspset: reply line.

A simple example client server dialog.
% telnet localhost 12886
Trying 127.0.0.1...
Connected to localhost.localdomain.
Escape character is '^]'.
% version
version: exonerate-server 2.0.0
% dbinfo
dbinfo: dna softmasked 100000 1701 38113579
% lookup AA159529.1
lookup: 88065
% get info 88065
seqinfo: 62 2028 AA159529.1 zo72g05.s1 Stratagene pancreas (#937208) Homo sapiens cDNA
% get seq 88065
seq: NAACTCATCNTTTTCTGCTGNATCCTCTTCACCAGTTTGGGGGANGGCCTGCACTTCCANAG
% get subseq 88065 10 20
subseq: TTTTCTGCTGNATCCTCTTC
% set query NAACTCATCNTTTTCTGCTGNATCCTCTTCACCAGTTTGGGGGANGGCCTGCACTTCCANAG
ok: 62 2028
% get hsps
linecount: 15
hspset: 12423 1 349 41
hspset: 44900 1 356 47
hspset: 61781 1 358 41 36 392 26
hspset: 70065 1 349 41 36 383 26
hspset: 88065 1 1 61
hspset: 91032 1 357 41 36 391 26
hspset: 91442 1 350 41 36 384 26
hspset: 92971 1 348 41 36 382 26
hspset: 94311 1 375 41
hspset: 95381 1 346 41 36 380 26
hspset: 96808 10 385 32 36 410 26
hspset: 88449 18 11 22
hspset: 91036 6 6 56
hspset: 93736 36 400 26
% revcomp query
ok: query strand revcomp
% get hsps
linecount: 6
hspset: 12564 0 64 26 20 83 41
hspset: 61780 0 266 61
hspset: 29148 0 116 61
hspset: 25849 15 445 22
hspset: 93938 26 265 34
% exit
Connection closed by foreign host.

ENVIRONMENT
Not documented yet.

EXAMPLES
1. Example of creating a translated index and running a fast pro-
tein2genome search using exonerate-server

fasta2esd human.genomic.fasta human.genomic.esd esd2esi --translate yes hu-
man.genomic.esd human.genomic.trans.esi exonerate-server --port 1234 hu-
man.genomic.trans.esi exonerate pep.fasta localhost:1234 --model p2g --see-
drepeat 3 --geneseed 250

VERSION
This documentation accompanies version 2.2.0 of the exonerate package.

AUTHOR
Guy St.C. Slater. <guy@ebi.ac.uk>. See the AUTHORS file accompanying the
source code for a list of contributors.

AVAILABILITY
This source code for the exonerate package is available under the terms of
the GNU general public licence.

Please see the file COPYING which was distrubuted with this package, or
http://www.gnu.org/licenses/gpl.txt for details.

This package has been developed as part of the ensembl project. Please see
http://www.ensembl.org/ for more information.

Header And Logo

Peripheral Links

Site Navigation

FreeBSD Manual Pages

Header And Logo

Peripheral Links

Search

Site Navigation

FreeBSD Manual Pages