Tag: Candidate

ICSNPathway 1.1 – Identify Candidate Causal SNPs and Pathways from Genome-wide Association Study

ICSNPathway 1.1

:: DESCRIPTION

ICSNPathway is a web server developed to discover candidate causal SNPs and corresponding candidate causal pathways from genome-wide association study (GWAS).

::DEVELOPER

Bioinformatics Lab, Institute of Psychology, Chinese Academy of Sciences

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • Java

:: DOWNLOAD

  ICSNPathway

:: MORE INFORMATION

Citation

K. Zhang, S. Chang, et al. (2011).
“ICSNPathway: identify candidate causal SNPs and pathways from genome-wide association study by one analytical framework.”
Nucleic Acids Res. 39(suppl 2): W437-W443.

PEP-SiteFinder – Identify Candidate Protein-peptide Interaction Sites.

PEP-SiteFinder

:: DESCRIPTION

PEP-SiteFinder is a tool that will, given the structure of a protein and the sequence of a peptide, identify protein residues predicted to be at peptide-protein interface.

::DEVELOPER

PEP-SiteFinder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces.
Saladin A, Rey J, Thévenet P, Zacharias M, Moroy G, Tufféry P.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W221-6. doi: 10.1093/nar/gku404.

BALL-SNP – Combining Genetic and Structural Information to Identify Candidate Non-synonymous SNPs

BALL-SNP

:: DESCRIPTION

BALL-SNPgp is the extension of the proof-of-concept tool BALL-SNP, a software tool based on the Biochemical Algorithms Library (BALL), a molecular modeling framework, providing robust and sophisticated algorithms on structural bioinformatics. BALL-SNPgp enables the assessment of multiple non-synonymous single nucleotide polymorphisms (nsSNPs) in a single protein by visualizing the mutated residues within the wild type structure, collecting available pathogenicity information from different databases, predicting binding pockets, protein stability changes and pathogenicity, as well as performing a cluster analysis on comprised amino acid substitutions

::DEVELOPER

Chair for clinical bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • BALL

:: DOWNLOAD

 BALL-SNPgp

:: MORE INFORMATION

Citation:

BALL-SNP: combining genetic and structural information to identify candidate non-synonymous single nucleotide polymorphisms.
Mueller SC, Backes C, Kalinina OV, Meder B, Stöckel D, Lenhof HP, Meese E, Keller A.
Genome Med. 2015 Jul 1;7(1):65. doi: 10.1186/s13073-015-0190-y.

HGTector 2.0b2 – Detection of Candidate HGT-derived Genes

HGTector 2.0b2

:: DESCRIPTION

HGTector is a computational pipeline for genome-wide detection of putative horizontal gene transfer (HGT) events based on sequence homology search hit distribution statistics.

::DEVELOPER

Qiyun Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 HGTector

:: MORE INFORMATION

Citation

BMC Genomics. 2014 Aug 26;15:717. doi: 10.1186/1471-2164-15-717.
HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers.
Zhu Q, Kosoy M, Dittmar K.

TepiTool – Computational Prediction of T Cell Epitope Candidates

TepiTool

:: DESCRIPTION

The Tepitool provides prediction of peptides binding to MHC class I and class II molecules.

::DEVELOPER

the IEDB Solutions Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TepiTool

:: MORE INFORMATION

Citation

TepiTool: A Pipeline for Computational Prediction of T Cell Epitope Candidates.
Paul S, Sidney J, Sette A, Peters B.
Curr Protoc Immunol. 2016 Aug 1;114:18.19.1-18.19.24. doi: 10.1002/cpim.12.

CandiSSR – Identifying Candidate Polymorphic SSRs Based on Multiple Assembled Sequences

CandiSSR

:: DESCRIPTION

CandiSSR is a new pipeline to automatically identify the candidate polymorphic SSRs for a given species or genus based on their assembled sequences.

::DEVELOPER

Enhua Xia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • BioPerl

:: DOWNLOAD

 CandiSSR

:: MORE INFORMATION

Citation

CandiSSR: An Efficient Pipeline used for Identifying Candidate Polymorphic SSRs Based on Multiple Assembled Sequences.
Xia EH, Yao QY, Zhang HB, Jiang JJ, Zhang LP, Gao LZ.
Front Plant Sci. 2016 Jan 7;6:1171. doi: 10.3389/fpls.2015.01171.

MORPH / MORPH-R 10.7 – MOdule guided Ranking of Candidate PatHway Genes

MORPH / MORPH-R 10.7

:: DESCRIPTION

MORPH is an algorithm for revealing missing genes in biological pathways, and demonstrate its capabilities

MORPH-R is Morph R package.

::DEVELOPER

Ron Shamir’s lab and Eleanore Wurtzel’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 MORPH , MORPH-R

:: MORE INFORMATION

Citation

Tzfadia, O., Amar, D., Bradbury, L.M.T., Wurtzel, E.T., and Shamir, R. (2012)
The MORPH algorithm: ranking candidate genes for membership in Arabidopsis thaliana and Solanum lycopersicum pathways.
Plant Cell. 2012 Nov;24(11):4389-406. doi: 10.1105/tpc.112.104513.

Physiol Plant. 2015 Jan 27. doi: 10.1111/ppl.12326. [Epub ahead of print]
The MORPH-R web server and software tool for predicting missing genes in biological pathways.
Amar D, Frades I, Diels T, Zaltzman D, Ghatan N, Hedley PE, Alexandersson E, Tzfadia O, Shamir R.

Exit mobile version