Source: fasta3 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller Section: science Priority: optional Build-Depends: debhelper-compat (= 12), libsimde-dev Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/fasta3 Vcs-Git: https://salsa.debian.org/med-team/fasta3.git Homepage: https://fasta.bioch.virginia.edu Rules-Requires-Root: no Package: fasta3 Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: ${perl:Depends}, libdbi-perl, libwww-perl, libjson-perl, libhtml-tableextract-perl, libxml-twig-perl, liburi-encode-perl, libdbd-mysql-perl, python3-mysqldb, ncbi-blast+, bedtools Description: tools for searching collections of biological sequences The FASTA programs find regions of local or global similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. Other programs provide information on the statistical significance of an alignment. Like BLAST, FASTA can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. . * Protein - Protein-protein FASTA - Protein-protein Smith-Waterman (ssearch) - Global Protein-protein (Needleman-Wunsch) (ggsearch) - Global/Local protein-protein (glsearch) - Protein-protein with unordered peptides (fasts) - Protein-protein with mixed peptide sequences (fastf) . * Nucleotide - Nucleotide-Nucleotide (DNA/RNA fasta) - Ordered Nucleotides vs Nucleotide (fastm) - Un-ordered Nucleotides vs Nucleotide (fasts) . * Translated - Translated DNA (with frameshifts, e.g. ESTs) vs Proteins (fastx/fasty) - Protein vs Translated DNA (with frameshifts) (tfastx/tfasty) - Peptides vs Translated DNA (tfasts) . * Statistical Significance - Protein vs Protein shuffle (prss) - DNA vs DNA shuffle (prss) - Translated DNA vs Protein shuffle (prfx) . * Local Duplications - Local Protein alignments (lalign) - Plot Protein alignment "dot-plot" (plalign) - Local DNA alignments (lalign) - Plot DNA alignment "dot-plot" (plalign) . This software is often used via a web service at the EBI with readily indexed reference databases at http://www.ebi.ac.uk/Tools/fasta/. Package: fasta3-doc Architecture: all Multi-Arch: foreign Section: doc Depends: ${misc:Depends} Breaks: fasta3 (<< 36.3.8h) Replaces: fasta3 (<< 36.3.8h) Description: user guide for FASTA tools The FASTA programs find regions of local or global similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. Other programs provide information on the statistical significance of an alignment. Like BLAST, FASTA can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. . The use of the package's many binaries and the equally representated conceptual approaches towards sequence analyses are summarised in this PDF.