:: DESCRIPTION
GWAS Pathway Identifier combines GWAS(Genome-Wide Accociation Studies) and pathway data as well as known and predicted protein-interaction data to identify disease specific SNP sets.
::DEVELOPER
the Interfaculty Institute for Biomedical Informatics (IBMI)
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Refge is a Global Alliance for Genomics and Health API specification to access reference sequences and sub-sequences using an identifier derived from the sequence itself.
::DEVELOPER
Sheffield lab of computational biology
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Yates AD, Adams J, Chaturvedi S, Davies RM, Laird M, Leinonen R, Nag R, Sheffield NC, Hofmann O, Keane TM.
Refget: standardised access to reference sequences.
Bioinformatics. 2021 Jul 14:btab524. doi: 10.1093/bioinformatics/btab524. Epub ahead of print. PMID: 34260694.
:: DESCRIPTION
PClust is a scalable parallel software for detecting dense subgraphs.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
C. Wu, A. Kalyanaraman.
An efficient parallel approach for identifying protein families in large-scale metagenomic data sets.
Proc. ACM/IEEE Supercomputing Conference (SC’08), Austin, TX, November 15-21. pp. 1-10. 2008
:: DESCRIPTION
Kinannote identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine/threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com. If the user inputs a complete proteome, additional modules evaluate the completeness of the kinome and place it in context with reference kinomes.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Oct 1;29(19):2387-94. doi: 10.1093/bioinformatics/btt419. Epub 2013 Jul 31.
Kinannote, a computer program to identify and classify members of the eukaryotic protein kinase superfamily.
Goldberg JM, Griggs AD, Smith JL, Haas BJ, Wortman JR, Zeng Q.
:: DESCRIPTION
EDCNN is a software to identify protein-RNA interactions by synergizing evolutionary optimization with gradient
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Wang Y, Yang Y, Ma Z, Wong KC, Li X.
EDCNN: Identification of Genome-Wide RNA-binding Proteins Using Evolutionary Deep Convolutional Neural Network.
Bioinformatics. 2021 Oct 25:btab739. doi: 10.1093/bioinformatics/btab739. Epub ahead of print. PMID: 34694393.
:: DESCRIPTION
RHybridFinder (RHF) is an R package to process immunopeptidomic data for putative hybrid peptide discovery
::DEVELOPER
Frederic Saab <frederic.saab at umontreal.ca>
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Saab F, Hamelin DJ, Ma Q, Kovalchik KA, Sirois I, Faridi P, Li C, Purcell AW, Kubiniok P, Caron E.
RHybridFinder: An R package to process immunopeptidomic data for putative hybrid peptide discovery.
STAR Protoc. 2021 Oct 21;2(4):100875. doi: 10.1016/j.xpro.2021.100875. PMID: 34746858; PMCID: PMC8551247.
:: DESCRIPTION
SnackNTM is a free software for Nontuberculous mycobacteria(NTM) identification.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Kim YG, Jung K, Kim S, Kim MJ, Lee JS, Park SS, Seong MW.
SnackNTM: An Open-Source Software for Sanger Sequencing-based Identification of Nontuberculous Mycobacterial Species.
Ann Lab Med. 2022 Mar 1;42(2):213-248. doi: 10.3343/alm.2022.42.2.213. PMID: 34635615; PMCID: PMC8548243.
:: DESCRIPTION
HaploBlock is a software program which provides an integrated approach to haplotype block identification, haplotyping SNPs (or haplotype phasing, resolution or reconstruction) and linkage disequilibrium (LD) mapping (or genetic association studies). HaploBlock is suitable for high density haplotype or genotype SNP marker data and is based on a statistical model which takes account of recombination hotspots, bottlenecks, genetic drift and mutations and has a Markov Chain at its core.
::DEVELOPER
Laboratory of Computational Biology , Technion
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
G. Greenspan* and D. Geiger
High Density Linkage Disequilibrium Mapping using Models of Haplotype Block Variation
Bioinformatics (2004) 20 (suppl 1): i137-i144.
:: DESCRIPTION
PIUS is an open source tool that performs peptide identification from tandem mass spectrograms using the six-frame translation of the complete genome. Differently from peptidomics methods that also allow a search against the complete genome, PIUS does not limit analysis of the genome to a small set of sequences that match a list of de novo reconstructions. Instead, it performs an exhaustive scan of the translation of the six reading frames of the complete genome. Therefore, this search is not biased towards a subset of candidates.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Aug 1;29(15):1913-4. doi: 10.1093/bioinformatics/btt298. Epub 2013 May 24.
PIUS: peptide identification by unbiased search.
Costa EP1, Menschaert G, Luyten W, De Grave K, Ramon J.
:: DESCRIPTION
AUDACITY is novel computational approach for the identification of Runs of Homozygosity by using VCF files from whole-exome and whole-genome sequencing data generated by second generation sequencing technologies.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Magi A, Giangregorio T, Semeraro R, Carangelo G, Palombo F, Romeo G, Seri M, Pippucci T.
AUDACITY: A comprehensive approach for the detection and classification of Runs of Homozygosity in medical and population genomics.
Comput Struct Biotechnol J. 2020 Jul 14;18:1956-1967. doi: 10.1016/j.csbj.2020.07.003. PMID: 32774790; PMCID: PMC7394861.
