BBTools for bioinformatician !
...directly in BBMap, or with pileup, if you already have a sam file. For example: Code: $ pileup.sh in=mapped.sam covstats=coverage.txt Calculating coverage of the genome Pro...2283 days ago
2475 days ago
Seal: SEquence ALignment evaluation suite
...del rate. Applying alignment tools to the genome and the reads through a standardized interface. Parsing the output of the alignment tool and calculating the number of reads that were...2326 days ago
3933 days ago
List of In-silico Binding Site Prediction Tools
...surface and those in the core of the protein. In order to differentiate between such buried residues, we describe a computational procedure for calculating the depth of a residue from t...3756 days ago
Edit distance application in bioinformatics !
...o array of arrays my $css_str_ref = CSS_Sorted( $STR1, $STR2 ); # ref to array of strings There are many different modules on CPAN for calculating the edit distance between two...2353 days ago
2135 days ago
Tags: %MinMax, tool, calculating, synonymous, codon, usage, impact, protein, folding
2186 days ago
OrthoANI: An improved algorithm and software for calculating average nucleotide identity
OAT uses OrthoANI to measure the overall similarity between two genome sequences. ANI and OrthoANI are comparable algorithms: they share the same species demarcation cut-off at 95~96% and large comparison studies have demonstrated both algorithms to produce near identical reciprocal similarities....Tags: OrthoANI, improved, algorithm, software, calculating, average, nucleotide, identity, ANI
1983 days ago