:: DESCRIPTION
ASSIST is an application for the detection of catalytic sites in unknown function proteins.
::DEVELOPER
the Theoretical Biology and Bioinformatics Laboratory
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Apr 1;30(7):1022-4. doi: 10.1093/bioinformatics/btt664. Epub 2013 Nov 15.
ASSIST: a fast versatile local structural comparison tool.
Caprari S, Toti D, Viet Hung L, Di Stefano M, Polticelli F.
:: DESCRIPTION
gSearch is a fast and flexible general search tool for whole-genome sequencing
::DEVELOPER
Soongsil University Machine Learning Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
gSearch: a fast and flexible general search tool for whole-genome sequencing.
Song T, Hwang KB, Hsing M, Lee K, Bohn J, Kong SW.
Bioinformatics. 2012 Aug 15;28(16):2176-7. doi: 10.1093/bioinformatics/bts358
:: DESCRIPTION
TandemSWAN (Tandem Structure Word ANalyzer) is the tool for Divergent Tandem Repeats Searching.It is based on calculation of the repeat statistical significance and identifies the length of the repeated unit and the number of repetitions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2006 Mar 15;22(6):676-84. Epub 2006 Jan 10.
Short fuzzy tandem repeats in genomic sequences, identification, and possible role in regulation of gene expression.
Boeva V, Regnier M, Papatsenko D, Makeev V.
:: DESCRIPTION
YASS (Yet Another Similarity Searcher) is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments). Like most of the heuristic DNA local alignment software (BLAST, FASTA, PATTERNHUNTER, BLASTZ …), YASS uses seeds to detect potential similarity regions, and then tries to extend them to actual alignments. This genomic search tool uses multiple transition constrained spaced seeds that enable to search more fuzzy repeats, as non-coding DNA/RNA. Another simple, but interesting feature is that you can specify the seed pattern used in the search step
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
L. Noe, G. Kucherov,
YASS: enhancing the sensitivity of DNA similarity search, 2005,
Nucleic Acids Research, 33(2):W540-W543.
:: DESCRIPTION
Annokey is a command line tool for annotating gene lists with the results of a key-term search of the NCBI Gene database and linked PubMed article abstracts. Its purpose is to help users prioritise genes by relevance to a domain of interest, such as “breast cancer” or “DNA repair” etcetera. The user steers the search by specifying a ranked list of keywords and terms that are likely to be highly correlated with their domain of interest.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
ExactSearch is a web tool which enables plant biologists to search for DNA motifs in the proximal promoters, and 3′ untranslated regions of all genes from 50 genome-sequenced plant species.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
ExactSearch: a web-based plant motif search tool.
Gunasekara C, Subramanian A, Avvari JV, Li B, Chen S, Wei H.
Plant Methods. 2016 Apr 28;12:26. doi: 10.1186/s13007-016-0126-6.
:: DESCRIPTION
Nucleosome is web-based nucleosome map visual browser backed up by BWT-based pattern searches. It can be used for other kinds of high-throughput genomic data as well.
::DEVELOPER
The VisUsal (Visual Analytics and Information Visualization, Universidad de Salamanca) group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Santamaría, R., Therón, R., Durán, L., García, A., González, S., Sánchez, M., & Antequera, F. (2019).
Genome-wide search of nucleosome patterns using visual analytics.
Bioinformatics, 35(13), 2185-2192
:: DESCRIPTION
HaMStR (Hidden Markov Model based Search for Orthologs using Reciprocity)is a Hidden Markov Model based search tool to screen EST sequence data for the presence of putative orthologs to a pre-defined set of genes.
::DEVELOPER
the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
BMC Evol Biol. 2009 Jul 8;9:157.
HaMStR: profile hidden markov model based search for orthologs in ESTs.
Ebersberger I, Strauss S, von Haeseler A.
:: DESCRIPTION
GWFASTA (Genome Wise Sequence Similarity Search using FASTA) allows user to search their sequence against sequenced genomes and their product proteome. This integrate various tools which allows analysys of FASTA search
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Issac, B. and Raghava, G. P. S.(2002)
GWFASTA: A server for FASTA search in Eukaryotic and Microbial genomes.
BioTechniques 33(3):548-556.
:: DESCRIPTION
BlastR is a new method for searching Non-Coding RNAs in databases. The strategy we adopted relies on the use of the mutual information embedded in di-nucleotides. We have shown that this approach has better sensitivity and specifity than other softwares with comparable computational cost. BlastR package is a perl wrapper for BlastP and it is part of the T-Coffee distribution.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bussotti G, Raineri E, Erb I, Zytnicki M, Wilm A, Beaudoing E, Bucher P, Notredame C.
BlastR—fast and accurate database searches for non-coding RNAs
Nucleic Acids Res. 2011 Sep 1;39(16):6886-95.
