getGenomewideAln.pl

• NAME
• SYNOPSIS
• OPTIONS
• DESCRIPTION
• EXAMPLES
• AUTHORS
• AVAILABILITY

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NAME

getGenomewideAln.pl - part of the NcDNAlign alignment pipeline, step (2)

Wraps a pairwise BLAST search of the target genome against all other organisms listed in the configurations file.

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SYNOPSIS

getGenomewideAln.pl [options]

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OPTIONS

-c, --conf FILE

Path to central NcDNAlign configuration file

-s, --silent [0|1]

Silent mode, avoid printing to STDOUT 0=OFF (Default), 1=ON

-v, --version

Prints version information and exits.

-h, --help

Prints a short help message and exits.

--man

Prints a detailed manual page and exits.

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DESCRIPTION

The script performs a pairwise nucleotide BLAST search using BLASTN to align the reference sequence heuristically against all other species. The best hit for each query subsequence is retained if the EVALUE of the BLAST search does not exceed the EVALUE-threshold and the query length is larger than a certain minimal length. Both thresholds are given in the config file. Results of the BLAST search are stored at the directory 'blast'.

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EXAMPLES

$ getGenomewideAln.pl -c config-file.cfg

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AUTHORS

Dominic Rose (dominic@bioinf.uni-leipzig.de)

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AVAILABILITY

http://www.bioinf.uni-leipzig.de/Software/NcDNAlign/