realign.pl

NAME
SYNOPSIS
OPTIONS
DESCRIPTION
EXAMPLES
AUTHORS
AVAILABILITY

NAME

realign.pl - part of the NcDNAlign alignment pipeline, step (4)

Realignment of prior BLAST hits.

SYNOPSIS

realign.pl [options]

OPTIONS

-c, --conf FILE: Path to central NcDNAlign configuration file [REQUIRED]
-o, --out [0|1]: Printing detailed results at STDOUT ON(1) or OFF(0). Default: 0.
-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.

DESCRIPTION

Traditionally, MSAs are set up by pairwise alignments. We follow this strategy by grouping corresponding BLAST HSPs to one single MSA. Therefore, all HSPs are sorted according to the loci of the reference genome. Afterwards, one 'best' subject sequence is selected for each reference locus that overlaps the reference. It is ensured that every new subject sequence overlaps with all previous ones of the hitherto MSA. FThe minimal length for acceptance of an alignment is defineable. We recommend a value of 40 nt for ncRNA prediction and gene-finding on a genome-wide scale. Optionally, alignable subsequences can be enlarged by a certain user-defined flanking region. This compensates putative BLAST alignment errors, whenever initial seed alignments are not sufficiently extended to HSPs. Finally, MSAs of all accepted regions are computed using DIALIGN. Furthermore, the script creates a BED file 'gwAln.bed' keeping the coordinates of the alignment input respectively initial BLAST hits.

Be careful: A temporary file 't.NcDNAlign' must be createable in the screens' directory!