NAME

annotate-ali.pl - Annotate sequences by homology search using BLAST

VERSION

version 0.251060

USAGE

annotate-ali.pl <infiles> --database=<file> --regex=<regex> [options]

REQUIRED ARGUMENTS

<infiles>

Path to input ALI files [repeatable argument].

--ref-file [=] <file> | --database [=] <file>

Path to the FASTA file containing the sequence database.

--[ref-]regex [=] <regex>

Regular expression for capturing the reference seq id fragment that has to be used for annotating infile seq ids.

OPTIONS

--evalue [=] <float>

E-value threshold for annotating a sequence [default: 1e-10].

--identity [=] <number>

Identity threshold for annotating a sequence [default: 0]. When specified as a fraction between 0 and 1 (included), it is first multiplied by 100 to be interpreted in percentage.

--max-hits [=] <number>

Number of hits to return for each query (BLAST -max_target_seqs option) [default: 10]. Mostly useful in conjunction with the --hit-list option.

--tblastx

Enforce using TBLASTX (instead of the auto-selected BLASTN) when both the infile and the database contain nucleotide sequences [default: no].

--ann-file

Write an annotated version (with prefixed ids) of the infile [default: no].

--hit-list

Print a list of id/hit pairs (at the specified E-value and identity thresholds) instead of the standard annotation report [default: no].

--out[-suffix] [=] <suffix>

Suffix to append to infile basenames for deriving outfile names [default: -ann]. When not specified, outfile names are taken from infiles but original infiles are preserved by being appended a .bak suffix.

--[no]guessing

[Don't] guess whether sequences are aligned or not [default: yes].

--version

--usage

--help

--man

Print the usual program information

AUTHOR

Denis BAURAIN <denis.baurain@uliege.be>

CONTRIBUTOR

Valerian LUPO <valerian.lupo@uliege.be>

COPYRIGHT AND LICENSE

This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.