Documentation
Manual Pages
- ncDNAlign.1.cutSequences.pl
- ncDNAlign.2.getGwAln.pl
- ncDNAlign.3.mergeGwAln.pl
- ncDNAlign.4.realign.pl
- ncDNAlign.5.trimAln.pl
mergeGenomewideAln.pli
NAME
mergeGenomewideAln.pl - part of the NcDNAlign alignment pipeline, step (3)
Filtering and merging of BLAST hits (required blast input format: tabular output by -m 8). Ensures that all compatible hits in same genomic region (distance <= --dist) are merged to span complete genes.
SYNOPSIS
mergeGenomewideAln.pl [options]
OPTIONS
- -c, --conf FILE
-
Path to central NcDNAlign configuration file [REQUIRED]
- -d, --dist INTEGER
-
Maximal nucleotide distance between BLAST HSPs to be considered as neighboured and, thus, potentially merged. Default: 30.
- -o, --out [0|1]
-
Printing detailed results at STDOUT
ON(1)or OFF(0). Default: 0. - -t, --test [0|1]
-
Should the results be verified? Enable consistency checks, e.g. ensure that each inputted HSP is also outputted (1=YES, 0=NO). 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
Prevalently, sequences are less conserved in regions without base pair interactions, which might prevent the aligning procedures in getGenomwideAln.pl from extending the sequence alignment into such regions. Due to rearrangement, deletion, and duplication events during evolution, not all single local alignments lead to consistent global alignments. Therefore, compatible adjacent BLAST HSPs with a maximal distance of 30 nt are combined to ensure that heuristic global alignments span complete genes. Only appropriate HSPs exceeding a certain EVALUE-cutoff are reported and make it into a consecutive merging process. This merging algorithm is about calculating consistence graphs. Their maximal cliques define valid sets of combinable alignments. Output is written to *.merged files. They contain the merged BLAST hits.
EXAMPLES
$ mergeGenomewideAln.pl -c config-file.cfg
AUTHORS