exonerate-server(1)

💖 exonerate-server(1) 💖

okay bestie, welcome to the sequence comparison server page for exonerate. yes, this is exonerate-server(1), the server side of the whole situation. grab a strawberry 🍓 and let's get into it.

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✨ SYNOPSIS ✨

exonerate-server [ options ] <index path>

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🌸 DESCRIPTION 🌸

exonerate-server is a multi-threaded server for the exonerate sequence alignment program. no cap.

it takes a set of sequences plus a matching index file, and it uses them to allow fast of large datasets. (yes, the sentence is like that in the original, we're keeping it exactly, the vibe is intact 💅)

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🦋 OVERVIEW 🦋

okay so here's the whole journey, step by step, main character energy:

Step one: you gotta make an .esd file out of your sequence files. .esd means Exonerate Sequence Dataset file, and it can group together any set of sequences where each sequence has unique identifiers. you do this with the fasta2esd utility:

fasta2esd genome.fasta genome.esd

Step two: you make an .esi file from the .esd file. .esi means Exonerate Sequence Index file, and it holds an index or a set of indices that correspond to a particular dataset. that's the esd2esi utility's whole job:

esd2esi genome.esd genome.esi

Step three: once your .esi file exists, you can start the exonerate-server:

exonerate-server genome.esi

Step four: while the server is running, you can use exonerate to query it — you just swap out the target sequences on the command line for the name of the server and the port number. the default port number for exonerate-server is 12886. periodt.

exonerate query.fasta localhost:12886

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💅 OPTIONS 💅

some of the command line options for exonerate-server are literally the same as the ones for the

• exonerate client, and those are documented in the man page for exonerate. the other options, the ones that are exonerate-server-specific, are documented right here. 🫶
• --port <port> — specify the port the server should listen on. by default exonerate-server listens on port 12886, but you can absolutely pick a different port with this option.
• --input <index file> — specify the index file to use when the server starts. this option is mandatory (yes, required, no skipping it 🙈). 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 the fast performance that would otherwise be hampered by frequent disk accesses. this option lets you turn index and sequence preloading off, which lets the server run much more slowly, but with faster startup and a smaller memory footprint.

not advised to turn preloading off unless you're testing or debugging the server. seriously bestie, leave it on 💀

• --maxconnections <count> — the server is multithreaded, and this option sets the number of client processes 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 the server is running on.
• --verbosity <level> — set the verbosity level for the server. if it's zero, the server will be silent, and the higher the number, the more messages the server reports about what's happening.

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🌈 INTERFACE 🌈

this section documents the communication interface between

• the client and server. the interface is documented for people who want 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's possible to use telnet as a client for testing a server. iconic, honestly.

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 database
• <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 omitted.

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 implemented 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.

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⭐ ENVIRONMENT ⭐

Not documented yet. (bestie we simply do not know yet 🙈)

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🔥 EXAMPLES 🔥

1. Example of creating a translated index and running a fast protein2genome search using exonerate-server

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

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👑 VERSION 👑

this documentation accompanies version 2.2.0 of the exonerate package.

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💜 AUTHOR 💜

Guy St.C. Slater. <guy@ebi.ac.uk>.

See the AUTHORS file accompanying the source code for a list of contributors.

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🌸 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.

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🦋 SEE ALSO 🦋

exonerate(1), (yes that's it, that's the list 💖)

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and that's the whole page bestie!! 🎀 this little beauty is exonerate-server from the exonerate package, dated January 2008, and it's serving that classic exonerate-server(1) manual-page energy. go forth and preload those indices, ilysm 🫶✨