:: DESCRIPTION
PgSA (Pseudogenome Suffix Array) is a compact index for collections of reads from sequencing. It allows to ask for presence of k-mers in the reads.
::DEVELOPER
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2015 Jul 16;10(7):e0133198. doi: 10.1371/journal.pone.0133198. eCollection 2015.
Indexing Arbitrary-Length k-Mers in Sequencing Reads.
Kowalski T, Grabowski S, Deorowicz S.
:: DESCRIPTION
MuGI is a compressed index of collections of genomes of the same species. It allows to ask for both exact and approximate queries. The input data must be given as a reference sequence and Variant Call Format (VCF) file describing the differences between individual genomes and reference genome.
::DEVELOPER
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Indexes of large genome collections on a PC.
Danek A, Deorowicz S, Grabowski S.
PLoS One. 2014 Oct 7;9(10):e109384. doi: 10.1371/journal.pone.0109384.
:: DESCRIPTION
RNAsifter is a non-rigorous filter for the rfam database, that is based on the abstract shape approach. It exploits the familily specific secondary structure, i.e. it computes shapes for the query-sequence and compares them to a precalculated shape-index. The exact matches deliver – hopefully only few – candiate families in which the query-sequence might fold. Membership for the candidate families is checked with the program cmsearch, afterwards.
::DEVELOPER
S. Janssen, J. Reeder and R. Giegerich.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
S. Janssen, J. Reeder and R. Giegerich.
Shape based indexing for faster search of RNA family databases.
BMC Bioinformatics. 2008 Feb 29;9:131.
:: DESCRIPTION
GEM Library (GEnome Multi-tool) is a set of very optimized tools for indexing/querying huge genomes/files. Provided so far are a very fast exhaustive mapper (the GEM mapper), an unconstrained split mapper (the GEM split mapper), and a very fast program to compute genome mappability (the GEM mappability).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
The program mpscan (Multi Pattern Scanner) is a software that performs Set Pattern Matching on nucleotitic sequences (DNA/RNA): it searches for a large set of patterns at once in a sequence.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Rivals E., Salmela L., Kiiskinen P., Kalsi P., Tarhio J.
mpscan: Fast Localisation of Multiple Reads in Genomes
Lecture Notes in BioInformatics (LNBI), Springer-Verlag, Vol. 5724, p. 246-260, 2009.
:: DESCRIPTION
HS (host specificity) provided here calculates an index of host specificity for parasites based on the number of species, genera, families, orders, and classes in which a species is found. It incorporates the hierarchical information about host distribution included in the Linnean hierarchy, but it is not explcitly tree based.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
