YASS (Yet Another Similarity Searcher) is a

free software Free software, libre software, libreware sometimes known as freedom-respecting software is computer software distributed open-source license, under terms that allow users to run the software for any purpose as well as to study, change, distribut ...

, 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 compound, organic molecules composed of a nitrogenous base, a pentose sugar and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both o ...

sequences, that is, it can search for similarities between

DNA Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...

RNA Ribonucleic acid (RNA) is a polymeric molecule that is essential for most biological functions, either by performing the function itself (non-coding RNA) or by forming a template for the production of proteins (messenger RNA). RNA and deoxyrib ...

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 for ...

and the output format includes the BLAST tabular output. YASS uses several ''transition-constrained'' spaced seed k-mers, 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 cloud computing service model where the provider offers use of application software to a client and manages all needed physical and software resources. SaaS is usually accessed via a web application. Unlike oth ...

on th
YASS web server
which produces a browser based dot-plot.

References

External links

Official website
Free bioinformatics software Computational biology {{Bioinformatics-stub

See also

References

External links