MitoSeek 1.3 – Extract Mitochondrial Genome information from Exome Sequencing data

MitoSeek 1.3

:: DESCRIPTION

MitoSeek is an open-source software tool to reliably and easily extract mitochondrial genome information from exome sequencing data. MitoSeek evaluates mitochondrial genome alignment quality, estimates relative mitochondrial copy numbers, and detects heteroplasmy, somatic mutation, and structural variance of the mitochondrial genome.

::DEVELOPER

Yan GuoJiang (River) Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 MitoSeek

:: MORE INFORMATION

Citation

Yan Guo, Jiang Li, Yu Shyr, David C. Samuels.
MitoSeek: Extracting Mitochondria Information and Performing High Throughput Mitochondria Sequencing Analysis.
Bioinformatics (2013) 29 (9): 1210-1211

Human Genome 1.0.2 – Obtain information about a known Gene

Human Genome 1.0.2

:: DESCRIPTION

The Human Genome App is designed so that a person can obtain information about a known gene or discover relationships between genes and diseases, syndromes or traits.

::DEVELOPER

Florence Haseltine

:: SCREENSHOTS

HumanGenome

:: REQUIREMENTS

  •  iPad

:: DOWNLOAD

 Human Genome

:: MORE INFORMATION

MetaCrop – Browsing and Working with Information from the MetaCrop database

MetaCrop

:: DESCRIPTION

MetaCrop is an Add-on to enable browsing of the content of the handcurated Metacrop database. Users can directly load hand-layouted pathway maps or metabolic network models to use for browsing, pathway exploration, data-mapping and analysis or use them for metabolic modelling. The user can also filter the pathway for species specific information, which will be visually highlighted.

::DEVELOPER

Matthias Klapperstueck and Klaus Hippe.

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 MetaCrop

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jan;40(Database issue):D1173-7. Epub 2011 Nov 15.
MetaCrop 2.0: managing and exploring information about crop plant metabolism.
Schreiber F, Colmsee C, Czauderna T, Grafahrend-Belau E, Hartmann A, Junker A, Junker BH, Klapperstück M, Scholz U, Weise S.

FASTR – Format for Concomitant Representation of RNA Sequence and Secondary Structure Information

FASTR

:: DESCRIPTION

FASTR is a novel storage format for concomitant representation of RNA sequence and structure.

::DEVELOPER

Bio-Sciences R&D Division, TCS Innovation Labs

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • RNAfold
  • JRE

:: DOWNLOAD

 FASTR

 

:: MORE INFORMATION

Citation

J Biosci. 2015 Sep;40(3):571-7.
FASTR: A novel data format for concomitant representation of RNA sequence and secondary structure information.
Bose T1, Dutta A, Mh M, Gandhi H, Mande SS.

MICO – Mutation Information Collector

MICO

:: DESCRIPTION

MICO is a meta-tool for automatically querying and collecting related information from multiple biology/bioinformatics enabled web servers with prediction capabilities.

::DEVELOPER

MICO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformation. 2014 Jul 22;10(7):469-71. doi: 10.6026/97320630010469. eCollection 2014.
MICO: A meta-tool for prediction of the effects of non-synonymous mutations.
Lee G1, Chen CF

Uniprot DAT File Parser 1.1.5483 – Read Uniprot (IPI) .Dat file and Parse out the information for each entry

Uniprot DAT File Parser 1.1.5483

:: DESCRIPTION

The Uniprot DAT File Parser can read a Uniprot (IPI) .Dat file and parse out the information for each entry, creating a tab delimited text file. Uniprot .Dat files can be obtained from EBI’s FTP site.

::DEVELOPER

Biological MS Data and Software Distribution Center , Pacific Northwest National Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Microsoft NET Framework 3.5

:: DOWNLOAD

 Uniprot DAT File Parser

:: MORE INFORMATION

GWIPS-viz – Genome Wide Information on Protein Synthesis

GWIPS-viz

:: DESCRIPTION

GWIPS-viz aims to provide on-line tools for the analysis and visualization of ribo-seq data obtained with the ribosome profiling technique

::DEVELOPER

GWIPS-viz team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Proteomics. 2015 Mar 3. doi: 10.1002/pmic.201400603.
GWIPS-viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms.
Michel AM1, Ahern AM, Donohue CA, Baranov PV.

BRISK – Biology-Related Information Storage Kit

BRISK

:: DESCRIPTION

BRISK is a package of several web-based data management tools that provide a cohesive data integration and management platform. It was specifically designed to provide the architecture necessary to promote collaboration and expedite data sharing between scientists.

::DEVELOPER

Genapha

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Apache
  • MySQL

:: DOWNLOAD

   BRISK

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Sep 1;27(17):2422-5. doi: 10.1093/bioinformatics/btr389. Epub 2011 Jun 27.
BRISK–research-oriented storage kit for biology-related data.
Tan A, Tripp B, Daley D.

ProCKSI 20080829 – Protein (Structure) Comparison, Knowledge, Similarity and Information

ProCKSI 20080829

:: DESCRIPTION

ProCKSI is a decision support system for protein structure comparison. It computes structural similarities using a variety of similarity comparison methods in order to produce a similarity consensus.

::DEVELOPER

ProCKSI team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ProCKSI: a decision support system for Protein (structure) Comparison, Knowledge, Similarity and Information.
Barthel D, Hirst JD, Błazewicz J, Burke EK, Krasnogor N.
BMC Bioinformatics. 2007 Oct 26;8:416.

PHASEBOOK 2.5 – Phasing Marker Genotypes using familial (LINKPHASE), population information

PHASEBOOK 2.5

:: DESCRIPTION

PHASEBOOK is an haplotyping programs package: LinkPHASE,HiddenPHASE, DualPHASE and DAGPHASE. The proposed methods work in two steps. First, haplotypes are reconstructed based on familial information (Mendelian segregation rules and linkage information) and next it fills in the gaps by applying a Hidden Markov Model (models from fastPHASE (Scheet and Stephens, 2006) or from Beagle (Browning and Browning, 2007)).

::DEVELOPER

Unit of Animal Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PHASEBOOK

:: MORE INFORMATION

Citation

LINKPHASE3: an improved pedigree-based phasing algorithm robust to genotyping and map errors.
Druet T, Georges M.
Bioinformatics. 2015 Jan 7. pii: btu859.

Druet & Georges, 2010
A Hidden Markov Model Combining Linkage and Linkage Disequilibrium Information for Haplotype Reconstruction and Quantitative Trait Locus Fine Mapping
Genetics. 2010 Mar;184(3):789-98.