Jul 20, 2023

Collection of programs for searching DNA and protein databases

Version 3 of the FASTA packages contains many programs for searching DNA and protein databases and one program prss3 for evaluating statistical significance from randomly shuffled sequences. Several additional analysis programs, including programs that produce local alignments, are available as part of version 2 of the FASTA package, which is available as the port biology/fasta.

FASTA is described in W. R. Pearson and D. J. Lipman 1988, “Improved Tools for Biological Sequence Analysis”, PNAS 852444-2448; W. R. Pearson 1996 “Effective protein sequence comparison” Meth. Enzymol. 266227-258; Pearson et. al. 1997 Genomics 4624-36; Pearson, 1999 Meth. in Molecular Biology 132185-219.

The FASTA3 suite is distributed freely subject to the condition that it may not be sold or incorporated into a commercial product.

Checkout these related ports:
  • Wise - Intelligent algorithms for DNA searches
  • Wfa2-lib - Exact gap-affine algorithm using homology to accelerate alignment
  • Vt - Discovers short variants from Next Generation Sequencing data
  • Vsearch - Versatile open-source tool for metagenomics
  • Viennarna - Alignment tools for the structural analysis of RNA
  • Velvet - Sequence assembler for very short reads
  • Vcftools - Tools for working with VCF genomics files
  • Vcflib - C++ library and CLI tools for parsing and manipulating VCF files
  • Vcf2hap - Generate .hap file from VCF for haplohseq
  • Vcf-split - Split a multi-sample VCF into single-sample VCFs
  • Unikmer - Toolkit for nucleic acid k-mer analysis, set operations on k-mers
  • Unanimity - Pacific Biosciences consensus library and applications
  • Ugene - Integrated bioinformatics toolkit
  • Ucsc-userapps - Command line tools from the UCSC Genome Browser project
  • Trimmomatic - Flexible read trimming tool for Illumina NGS data