PHAST 20141110 / PHASTER – Fast Phage Search tool

PHAST 20141110 / 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.

mrsFAST-Ultra 3.3.8 – 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.

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.

STRING 10 – Search Tool for the Retrieval of Interacting Genes/Proteins

STRING 10

:: DESCRIPTION

STRING (search tool for recurring instances of neighbouring genes) is a database and web resource dedicated to protein-protein interactions, including both physical and functional interactions. It weights and integrates information from numerous sources, including experimental repositories, computational prediction methods and public text collections, thus acting as a meta-database that maps all interaction evidence onto a common set of genomes and proteins.

::DEVELOPER

Bork Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

STRING v10: protein-protein interaction networks, integrated over the tree of life.
Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C.
Nucleic Acids Res. 2015 Jan;43(Database issue):D447-52. doi: 10.1093/nar/gku1003

Nucleic Acids Res. 2013 Jan;41(Database issue):D808-15. doi: 10.1093/nar/gks1094. Epub 2012 Nov 29.
STRING v9.1: protein-protein interaction networks, with increased coverage and integration.
Franceschini A1, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ.

STRING 8–a global view on proteins and their functional interactions in 630 organisms.
Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C.
Nucleic Acids Res. 2009 Jan;37(Database issue):D412-6. Epub 2008 Oct 21.

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored.
Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, von Mering C.
Nucleic Acids Res. 2011 Jan;39(Database issue):D561-8. Epub 2010 Nov 2.

STITCH 5.0 – Search Tool for Interactions of Chemicals and proteins

STITCH 5.0

:: DESCRIPTION

STITCH (search tool for interactions of chemicals)  is a resource to explore known and predicted interactions of chemicals and proteins.Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.

::DEVELOPER

Bork Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Web Browser / Linux

:: DOWNLOAD

 STITCH

:: MORE INFORMATION

Citation

STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data.
Szklarczyk D, Santos A, von Mering C, Jensen LJ, Bork P, Kuhn M.
Nucleic Acids Res. 2015 Nov 20. pii: gkv1277.

Nucleic Acids Res. 2014 Jan;42(Database issue):D401-7. doi: 10.1093/nar/gkt1207. Epub 2013 Nov 28.
STITCH 4: integration of protein-chemical interactions with user data.
Kuhn M1, Szklarczyk D, Pletscher-Frankild S, Blicher TH, von Mering C, Jensen LJ, Bork P.

STITCH: interaction networks of chemicals and proteins.
Kuhn M, von Mering C, Campillos M, Jensen LJ, Bork P
Nucleic Acids Res. 2008 Jan 15; 36: D684-8. Epub 2007 Dec 15; PubMed: 18084021.

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.

GEOmetadb 1.28.0 – GEO Microarray Search Tool

GEOmetadb 1.28.0

:: DESCRIPTION

GEOmetadb is an attempt to make access to the metadata associated with the NCBI Gene Expression Omnibus (GEO) samples, platforms, and datasets much more feasible for common biologists and bioinformatians/statistians.

::DEVELOPER

Jack Zhu , Sean Davis @NCI

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 GEOmetadb

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Dec 1;24(23):2798-800. doi: 10.1093/bioinformatics/btn520.
GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus.
Zhu Y, Davis S, Stephens R, Meltzer PS, Chen Y.

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)

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.

PLAST 1.0 – Parallel Local Alignment Search Tool for Database Comparison

PLAST 1.0

:: 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

Dominique Lavenier , Van Hoa Nguyen

:: 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).