Description: Given two genomes r and q, and a reference and query gene (or coordinate values), CNEFinder finds CNE matches between either the positions of the provided genes or coordinate values of the respective chromosomes of r and q.
Installation: To compile CNEFinder, please follow the instructions given in file INSTALL.
Usage: CNEFinder <options>
Standard (Mandatory):
-r, --ref-genome-file <str> FASTA reference genome filename.
-q, --query-genome-file <str> FASTA query genome filename.
-e, --exons-ref-file <str> TSV exon coordinates for reference genome filename.
-f, --exons-query-file <str> TSV exon coordinates for query genome filename.
-l, --min-seq-length <int> Minimum length of CNE.
-t, --sim-threshold <dbl> Threshold of similarity between sequences (0-1].
-o, --output-file <str> Output filename with CNEs identified in BED format.
Either 1. or 2.
1.Search using gene name:
-g, --ref-gene-file <str> TSV filename containing gene data for reference genome.
-n, --ref-gene-name <str> Name of gene in reference genome in which CNEs will be identified.
-j, --query-gene-file <str> TSV filename containing gene data for query genome.
-m, --query-gene-name <str> Name of gene in query genome in which CNEs will be identified.
2.Search using index position:
-y, --ref-chrom <str> Chromosome of reference genome.
-z, --query-chrom <str> Chromosome of query genome.
-a, --ref-start <int> Start CNE search from this position of reference sequence.
-b, --ref-end <int> End CNE search at this position of reference sequence.
-c, --query-start <int> Start CNE search from this position of query sequence.
-d, --query-end <int> End CNE search at this position of query sequence.
Optional:
-Q, --mem-length <int> Minimum length of maximal exact matches. Default:18.
-M, --merged-length <dbl> Minimum length (in terms of CNE length) of merged matches to be extended. Default:0.5.
-s, --ext-threshold <dbl> Threshold to further extend similarity threshold by. Default:0.05.
-u, --max-seq-length <int> Set a maximum length for the CNE. Default:2000.
-p, --repeat-regions <int> Choose 1 to filter repetitive regions of genomes or 0 otherwise. Default:1.
-v, --rev-complement <int> Choose 1 to compute CNEs for reverse complement or 0 otherwise. Default:0.
-x, --remove-overlaps <int> Choose 1 to remove overlapping CNEs or 0 otherwise. Default:1.
Number of threads:
-T, --threads <int> Number of threads to use. Default:1.
See https://github.com/lorrainea/CNEFinder/wiki for more help.
Citation:
L. A. K. Ayad, S. P. Pissis, D. Polychronopoulos:
CNEFinder: finding conserved non-coding elements in genomes.
Bioinformatics: 34(17): i743-i747 (2018)
License: GNU GPLv3 License; Copyright (C) 2017 Lorraine A. K. Ayad, Solon P. Pissis, Dimitris Polychronopoulos