:: DESCRIPTION
ssahaSNP is a polymorphism detection tool. It detects homozygous SNPs and indels by aligning shotgun reads to the finished genome sequence.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
ssahaSNP – a polymorphism detection tool on a whole genome scale
Z. Ning, M. Caccamo and J.C. Mullikin
Computational Systems Bioinformatics Conference, 2005. Workshops and Poster Abstracts. IEEE 2005;251 – 252
:: DESCRIPTION
ssahaEST is a software tool for very fast matching and alignment of ESTs/cDNAs to genomic DNA sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ning Z, Cox AJ and Mullikin JC
SSAHA: a fast search method for large DNA databases.
Genome research 2001;11;10;1725-9
:: DESCRIPTION
SSAHA (Sequence Search and Alignment by Hashing Algorithm) is a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences. Sequences in the database are preprocessed by breaking them into consecutive k-tuples ofk contiguous bases and then using a hash table to store the position of each occurrence of each k-tuple. Searching for a query sequence in the database is done by obtaining from the hash table the “hits” for each k-tuple in the query sequence and then performing a sort on the results. We discuss the effect of the tuple length k on the search speed, memory usage, and sensitivity of the algorithm and present the results of computational experiments which show that SSAHA can be three to four orders of magnitude faster than BLAST or FASTA, while requiring less memory than suffix tree methods. The SSAHAalgorithm is used for high-throughput single nucleotide polymorphism (SNP) detection and very large scale sequence assembly.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ning Z, Cox AJ and Mullikin JC
SSAHA: a fast search method for large DNA databases.
Genome research 2001;11;10;1725-9
:: DESCRIPTION
UBLAST and USEARCH are algorithms designed to enable high-throughput, sensitive search of very large sequence databases.
UBLAST searches for local alignments, USEARCH for global alignments. UBLAST and USEARCH are orders of magnitude faster than BLAST for some applications.
UCLUST is a clustering algorithm that uses USEARCH as a subroutine to achieve exceptional high speed and sensitivity.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2015 Jul 2. pii: btv401.
Error filtering, pair assembly, and error correction for next-generation sequencing reads.
Edgar RC, Flyvbjerg H
Edgar, R.C. (2010),
Search and clustering orders of magnitude faster than BLAST,
Bioinformatics.doi: 10.1093/bioinformatics/btq461
:: DESCRIPTION
PSI-BLAST-ISS is a standalone Unix-based tool designed to delineate reliable regions of sequence alignments as well as to suggest potential variants in unreliable regions. The region-specific reliability is assessed by producing multiple sequence alignments in different sequence contexts followed by the analysis of the consistency of alignment variants. The PSI-BLAST-ISS output enables the user to simultaneously analyze alignment reliability between query and multiple homologous sequences. In addition, PSI-BLAST-ISS can be used to detect distantly related homologous proteins.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Margelevicius M., Venclovas C. (2005)
PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability.
BMC Bioinformatics 6(1):185
