PLAST v2.3.1 – Parallel Local Alignment Search Tool for Database Comparison

PLAST v2.3.1

:: DESCRIPTION

PLAST (Parallel Local Alignment Search Tool for Database Comparison) is an intensive bank sequence comparison with a parallel version of BLAST-like software.The algorithm exploits two key parallel features of existing and future microprocessors: the SIMD programming model (SSE instruction set) and the multithreading concept (multicore). Compared to multithreaded BLAST software, tests performed on an 8-processor server have shown speedup ranging from 3 to 6 with a similar level of accuracy.

::DEVELOPER

PLAST team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac / Linux

:: DOWNLOAD

 PLAST

:: MORE INFORMATION

Citation

V.H. Nguyen, D. Lavenier,
PLAST: parallel local alignment search tool for database comparison,
BMC Bioinformatics, 2009 10(329).

GASSST 1.28 – Global Alignment Short Sequence Search Tool

GASSST 1.28

:: DESCRIPTION

GASSST (Global Alignment Short Sequence Search Tool) is 2-fold—achieving high performance with no restrictions on the number of indels with a design that is still effective on long reads.

::DEVELOPER

Dominique Lavenier , Guillaume Rizk , Damien Fleury

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GNU gcc compiler

:: DOWNLOAD

 GASSST

:: MORE INFORMATION

Citation

Guillaume Rizk and Dominique Lavenier
GASSST: global alignment short sequence search tool
Bioinformatics (2010) 26 (20): 2534-2540.

Chain-RNA 20120225 – Comparative ncRNA Search Tool Based on the Two-dimensional Chain Algorith

Chain-RNA 20120225

:: DESCRIPTION

Chain-RNA is an ncRNA structural alignment program based on extended two-dimensional chain algorithm. It has been applied to pairwise genome-scale ncRNA search.

::DEVELOPER

Yanni Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Chain-RNA

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2012 Oct 30. [Epub ahead of print]
Chain-RNA: A Comparative ncRNA Search Tool Based on the Two-dimensional Chain Algorithm.
Lei J, Techa-Angkoon P, Sun Y.

cdBEST – Chromatin Domain Boundary Element Search Tool

cdBEST

:: DESCRIPTION

cdBEST is a tool/software developed in Perl to search the chromatin domain boundary element sequences in 12 Drosophila species. cdBEST uses recognition sequences of boundary interacting proteins and looks for ‘motif clusters’ under a set of constrains to predict boundary element sequences. Apart from Drosophila, cdBEST can be used in several other insect genomes, where the boundary interacting proteins are conserved.

::DEVELOPER

Rakesh Mishra Lab

:: SCREENSHOTS

cdBEST

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Perl

:: DOWNLOAD

 cdBEST

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2012 May;40(10):4385-95. doi: 10.1093/nar/gks045. Epub 2012 Jan 28.
Chromatin domain boundary element search tool for Drosophila.
Srinivasan A1, Mishra RK.

mrFAST 2.6.1.0 – Micro Read Fast Alignment Search Tool

mrFAST 2.6.1.0

:: DESCRIPTION

mrFAST is micro-read Fast Alignment Search Tool. It is designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient manner.

::DEVELOPER

Eichler Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Complier

:: DOWNLOAD

  mrFAST

:: MORE INFORMATION

Can Alkan, Jeffrey M Kidd, Tomas Marques-Bonet, Gozde Aksay, Francesca Antonacci, Fereydoun Hormozdiari, Jacob O Kitzman, Carl Baker, Maika Malig, Onur Mutlu, S Cenk Sahinalp, Richard A Gibbs & Evan E Eichler
Personalized copy number and segmental duplication maps using next-generation sequencing
Nature Genetics 41, 1061 – 1067 (2009)

MaDCaT – Protein Structure Search tool

MaDCaT

:: DESCRIPTION

MaDCaT (Mapping of Distances for the Categorization of Topology) is a protein structure search tool

::DEVELOPER

Grigoryan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • C++ Compiler

:: DOWNLOAD

   MaDCaT

:: MORE INFORMATION

Citation:

Zhang J., Grigoryan G.,
Mining Tertiary Structural Motifs for Assessment of Designability“,
Methods Enzymol. 2013;523:21-40. doi: 10.1016/B978-0-12-394292-0.00002-3.

PhenoMeter 1.0 – Metabolome Database Search Tool

PhenoMeter 1.0

:: DESCRIPTION

The PhenoMeter is a metabolome database search tool that uses metabolite response patterns or metabolic phenotypes as queries, searching the MetabolomeExpress metabolomics database for significantly similar phenotypes and ranking them by similarity.

::DEVELOPER

PhenoMeter team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PhenoMeter: A Metabolome Database Search Tool Using Statistical Similarity Matching of Metabolic Phenotypes for High-Confidence Detection of Functional Links.
Carroll AJ, Zhang P, Whitehead L, Kaines S, Tcherkez G, Badger MR.
Front Bioeng Biotechnol. 2015 Jul 29;3:106. doi: 10.3389/fbioe.2015.00106.

mrsFAST-Ultra 3.4.2 – Micro-read Substitution-only Fast Alignment Search Tool

mrsFAST-Ultra 3.3.8

:: DESCRIPTION

mrsFAST (Micro-read Substitution-only Fast Alignment Search Tool ) is a cache oblivious mapper that is designed to map short reads to reference genome. mrsFAST maps short reads with respect to user defined error threshold. In this manual, we will show how to choose the parameters and tune mrsFAST with respect to the library settings. mrsFAST is designed to find ‘all’ the mappings for a given set of reads

::DEVELOPER

Eichler Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Complier

:: DOWNLOAD

 mrsFAST-Ultra

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2014 May 8.
mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications.
Hach F1, Sarrafi I, Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC.

Hach F, Hormozdiari F, Alkan C, Hormozdiari F, Birol I, Eichler EE, Sahinalp SC. (2010).
mrsFAST: a cache-oblivious algorithm for short-read mapping.
Nat Methods Aug;7(8):576-7.

Phobos 3.3.12 – Tandem Repeat search tool for Complete Genomes

Phobos 3.3.12

:: DESCRIPTION

Phobos is a tandem repeat search tool for complete genomes.PHOBOS can search for tandem repeats with a unit size of more than 5000 bp, which in the STAMP modules implies that primers can also be designed for minisatellites and tandem repeats with even longer units. Search settings and the output format of PHOBOS can be adjusted in a flexible manner, making it an ideal multipurpose tandem repeat search tool

::DEVELOPER

Dr. Christoph Mayer

:: SCREENSHOTS

::REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 Phobos

:: MORE INFORMATION

Citation

Kraemer, L., Beszteri, B., Gaebler-Schwarz, S., Held, C., Leese, F., Mayer, C., Poehlmann, K. & Frickenhaus, S. (2009)
STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design.
BMC Bioinformatics 10:41.

PHAST 20161213 / PHASTER – Fast Phage Search tool

PHAST 20161213 / PHASTER

:: DESCRIPTION

PHAST (PHAge Search Tool) is a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids.

PHASTER (PHAge Search Tool Enhanced Release) is a significant upgrade to the popular PHAST web server for the rapid identification and annotation of prophage sequences within bacterial genomes and plasmids,.

::DEVELOPER

the Wishart Research Group, University of Alberta

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

PHASTER: a better, faster version of the PHAST phage search tool.
Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y, Wishart DS.
Nucleic Acids Res. 2016 May 3. pii: gkw387.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W347-52. doi: 10.1093/nar/gkr485. Epub 2011 Jun 14.
PHAST: a fast phage search tool.
Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS.