HomSI v2.1 – Homozygous Stretch Identifier from Next-generation Sequencing data

HomSI v2.1

:: DESCRIPTION

HomSI is a homozygous stretch identifier from next-generation sequencing data.

::DEVELOPER

Advanced Genomics and Bioinformatic Research Group, İGBAM

:: SCREENSHOTS

HomSI

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

  HomSI

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Feb 1;30(3):445-7. doi: 10.1093/bioinformatics/btt686. Epub 2013 Dec 3.
HomSI: a homozygous stretch identifier from next-generation sequencing data.
Görmez Z1, Bakir-Gungor B, Sagiroglu MS.

RISCI – Repeat Induced Sequence Change Identifier

RISCI

:: DESCRIPTION

RISCI (Repeat Induced Sequence Changes Identifier) is a comprehensive, comparative genomics based, in silico subtractive hybridization tool, to identify differential insertions and associated subtle sequence changes like target site duplications (TSD), 3’ and 5′ flank transductions, insertion mediated deletions, recombination mediated deletions and polymorphism induced by transposons. Post insertion changes such as recombination mediated deletions and disruptions are also picked up by RISCI. It emulates subtractive hybridization in the sense that, only when the locus in the genomes is differential, does it report the sequence changes associated with the transposon insertion.

::DEVELOPER

Rakesh Mishra Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 RISCI

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Dec 26;11:609. doi: 10.1186/1471-2105-11-609.
RISCI–Repeat Induced Sequence Changes Identifier: a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify repeat induced sequence changes in closely related genomes.
Singh V1, Mishra RK.

Synergizer – Provide Translations of Biological Database Identifiers

Synergizer

:: DESCRIPTION

The Synergizer database is a growing repository of gene and protein identifier synonym relationships. This tool facilitates the conversion of identifiers from one naming scheme (a.k.a “namespace”) to another.

::DEVELOPER

Roth Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Synergizer for Perl , for Java

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Oct 1;24(19):2272-3. Epub 2008 Aug 12.
The Synergizer service for translating gene, protein and other biological identifiers.
Berriz GF, Roth FP.

NeuroPID 201503 – Neuropeptide-Precursor Identifier

NeuroPID 201503

:: DESCRIPTION

NeuroPID is a prediction tool for Neuropeptide Precursors (NPPs) and Neuromodulators

::DEVELOPER

The Sudarsky Center for Computational Biology – The Hebrew University of Jerusalem

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

NeuroPID: a classifier of neuropeptide precursors.
Karsenty S, Rappoport N, Ofer D, Zair A, Linial M.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W182-6. doi: 10.1093/nar/gku363.

iTAK 1.7 – Plant Transcription Factor & Protein Kinase Identifier and Classifier

iTAK 1.7

:: DESCRIPTION

iTAK is a program to identify plant transcription factors (TFs), transcriptional regulators (TRs) and protein kinases (PKs) from protein or nucleotide sequences and then classify individual TFs, TRs and PKs into different gene families. Identification and classification of TFs and TRs are based on the rules (required and forbidden protein domains of each gene family) described in Perez-Rodriguez et al (2010).

::DEVELOPER

Fei Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Perl
  • Bioperl

:: DOWNLOAD

 iTAK

:: MORE INFORMATION

InterProScan 5.39-77.0 – Protein Domains Identifier

InterProScan 5.39-77.0

:: DESCRIPTION

InterProScan is a tool that combines different protein signature recognition methods into one resource. The number of signature databases and their associated scanning tools, as well as the further refinement procedures, increases the complexity of the problem.

::DEVELOPER

EBI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 InterProScan

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 1;30(9):1236-40. doi: 10.1093/bioinformatics/btu031. Epub 2014 Jan 21.
InterProScan 5: genome-scale protein function classification.
Jones P1, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S.

Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R.
InterProScan: protein domains identifier
Nucleic Acids Res. 2005;33:W116-W120.

PICR – Protein Identifier Cross-Reference Service

PICR

:: DESCRIPTION

PICR  (Protein Identifier Cross-Reference) service, a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the UniProt Archive (UniParc) as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV) or Microsoft Excel (XLS) files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface.

::DEVELOPER

EBI.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 PICR

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2007 Oct 18;8:401.
The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.
Côté RG, Jones P, Martens L, Kerrien S, Reisinger F, Lin Q, Leinonen R, Apweiler R, Hermjakob H.