YASS (Yet Another Similarity Searcher)
is a
free software
Free software or libre software is computer software distributed under terms that allow users to run the software for any purpose as well as to study, change, and distribute it and any adapted versions. Free software is a matter of liberty, no ...
,
pairwise
sequence alignment software
This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequence alignment. See structural alignment software for structural alignment of proteins.
Database searc ...
for
nucleotide
Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules wi ...
sequences, that is, it can search for similarities between
DNA or
RNA
Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...
sequences. YASS accepts nucleotide sequences in either plain text or the
FASTA format
In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes. The format ...
and the output format includes the
BLAST
Blast or The Blast may refer to:
*Explosion, a rapid increase in volume and release of energy in an extreme manner
*Detonation, an exothermic front accelerating through a medium that eventually drives a shock front
Film
* ''Blast'' (1997 film), ...
tabular output. YASS uses several ''transition-constrained''
spaced seed
In bioinformatics, a spaced seed is a pattern of relevant and irrelevant positions in a sequence (biology), biosequence and a method of approximate string matching that allows for Base-pair substitution, substitutions. They are a straightforward ...
k-mers
In bioinformatics, ''k''-mers are substrings of length k contained within a biological sequence. Primarily used within the context of computational genomics and sequence analysis, in which ''k''-mers are composed of nucleotides (''i.e''. A, T, G, ...
, which allow considerably improved sensitivity. YASS can be used locally on a user's machine, or as
SaaS
Software as a service (SaaS ) is a software licensing and delivery model in which software is licensed on a subscription basis and is centrally hosted. SaaS is also known as "on-demand software" and Web-based/Web-hosted software.
SaaS is con ...
on th
YASS web server which produces a browser based
dot-plot.
See also
*
Sequence alignment software
This list of sequence alignment software is a compilation of software tools and web portals used in pairwise sequence alignment and multiple sequence alignment. See structural alignment software for structural alignment of proteins.
Database searc ...
*
PatternHunter PatternHunter is a commercially available homology search instrument software that uses sequence alignment techniques. It was initially developed in the year 2002 by three scientists: Bin Ma, John Tramp and Ming Li. These scientists were driven by ...
*
BLAST
Blast or The Blast may refer to:
*Explosion, a rapid increase in volume and release of energy in an extreme manner
*Detonation, an exothermic front accelerating through a medium that eventually drives a shock front
Film
* ''Blast'' (1997 film), ...
*
FASTA
FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985. Its legacy is the FASTA format which is now ubiquitous in bioinformatics.
History
The original FASTA program ...
*
JAligner JAligner is an open source Java implementation of the Smith-Waterman algorithm with Gotoh's improvementGotoh O (1982). An improved algorithm for matching biological sequences. ''J Mol Biol, 162:705-708''. for biological local pairwise sequence ali ...
References
External links
Official website
Free bioinformatics software
Computational biology
{{Bioinformatics-stub