Tag: Tools

GP 0.26 / Arka 0.11 – Sequence Manipulation tools

GP 0.26 / Arka 0.11

:: DESCRIPTION

GP and Arka are very leightweighed programs for manipulation of DNA / RNA / protein sequences. They are designed on one hand to run smoothly on older machines, and on the other — to faciliate processing of large numbers of sequence / data files. GP includes utilities to convert DNA / RNA to protein, determine codon usage / GC contents, promotor searches, Tm, searching for restriction sites, converting sequences into numerical representations and much more.

::DEVELOPER

Dr. January Weiner 3rd

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GP  / Arka

:: MORE INFORMATION

Logol – Pattern matching language and tools

Logol

:: DESCRIPTION

Logol is a language used to describe some patterns in a DNA/RNA/Protein sequence

::DEVELOPER

GenOuest

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Logol

:: MORE INFORMATION

Citation

Catherine Belleannée, Olivier Sallou, Jacques Nicolas.
Expressive Pattern Matching with Logol.
Application to the Modelling of -1 Ribosomal Frameshift events. JOBIM 2012- 13e Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2012, Rennes, France. pp. 5-14.

NeAT – Network Analysis Tools

NeAT

:: DESCRIPTION

NeAT is a toolbox for the analysis of biological networks, clusters, classes and pathways.

::DEVELOPER

NeAT Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 NeAT

:: MORE INFORMATION

Citation

Network Analysis Tools: from biological networks to clusters and pathways.
Brohée S, Faust K, Lima-Mendez G, Vanderstocken G, van Helden J.
Nat Protoc. 2008;3(10):1616-29. doi: 10.1038/nprot.2008.100.

Datasets2Tools – Repository and Search Engine for Bioinformatics Datasets, Tools and Canned Analyses

Datasets2Tools

:: DESCRIPTION

Datasets2Tools is a repository indexing 31,473 canned bioinformatics analyses applied to 6,431 datasets.

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

datasets2tools

:: MORE INFORMATION

Citation

Sci Data. 2018 Feb 27;5:180023. doi: 10.1038/sdata.2018.23.
Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses.
Torre D, Krawczuk P, Jagodnik KM, Lachmann A, Wang Z, Wang L, Kuleshov MV, Ma’ayan A.

Kraken 13-274 – Tools for Quality Control and Analysis of High-throughput Sequence data

Kraken 13-274

:: DESCRIPTION

Kraken consists of 3 tools ( Reaper ,  Tally  and  Sequence Imp ) designed to streamline the analysis of next-generation sequencing data. Although designed with small RNA sequence analysis in mind the tools can be used to address issues facing next-generation sequencing in general.

::DEVELOPER

Enright Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX /  Linux

:: DOWNLOAD

 Kraken

:: MORE INFORMATION

Citation:

Kraken: A set of tools for quality control and analysis of high-throughput sequence data
Matthew P.A. Davis, Stijn van Dongen, Cei Abreu-Goodger, Nenad Bartonicek and Anton J. Enright
Methods. 2013 Sep 1;63(1):41-9. doi: 10.1016/j.ymeth.2013.06.027. Epub 2013 Jun 29.

3FunMap 1.0 – Full-sib Family Functional Mapping tools

3FunMap 1.0

:: DESCRIPTION

3FunMap is a Windows software that can be used to construct genetic linkage maps and perform functional QTL mapping with molecular markers generated in a full-sib family. For linkage analysis, the software utilizes seven segregation types of markers to estimate the recombination and simultaneously predict the linkage phase between any two markers. It takes heuristic search method for ordering large number of markers of a linkage group by incorporating local ordering methods. Multi-locus linkage phases for the optimal order of each linkage group are predicted based on three-point linkage analysis.

::DEVELOPER

Center for Statistical Genetics, Penn State University

:: SCREENSHOTS

3FunMap

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 3FunMap

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jul 15;27(14):2006-8. doi: 10.1093/bioinformatics/btr306. Epub 2011 May 17.
3FunMap: full-sib family functional mapping of dynamic traits.
Tong C, Wang Z, Zhang B, Shi J, Wu R.

Biochemistry Lab Suite 3.0.1 – Tools Covering different fields of Biochemistry, Biology and Chemistry

Biochemistry Lab Suite 3.0.1

:: DESCRIPTION

Biochemistry Lab Suite app aims in helping scientists and students working in the field of mass spectrometry based proteomics, metabolomics, biochemistry, biology and chemistry but also aids in general lab work.

::DEVELOPER

rpor

:: SCREENSHOTS

BiochemistryLS

:: REQUIREMENTS

  • Android

:: DOWNLOAD

 Biochemistry Lab Suite 

:: MORE INFORMATION