:: DESCRIPTION
SatFind – C-program for Finding Satellites in Genomes
::DEVELOPER
the Algorithmics and Genetics Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2013 Apr 24;8(4):e62221. doi: 10.1371/journal.pone.0062221.
A satellite explosion in the genome of holocentric nematodes.
Subirana JA, Messeguer X.
:: DESCRIPTION
DisLocate is a a two-step method based on machine learning models for predicting both the bonding state and the connectivity patterns of cysteine residues in a protein chain.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Aug 15;27(16):2224-30. Epub 2011 Jun 29.
Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization.
Savojardo C, Fariselli P, Alhamdoosh M, Martelli PL, Pierleoni A, Casadio R.
:: DESCRIPTION
CleaveLand is a command-line executed pipeline for finding cleaved small RNA targets using degradome data (also known as PARE [parallel analysis of RNA ends] and GMUCT [genome-wide mapping of uncapped transcripts]). Provided with a set of degradome data, a list of small RNA queries, a reference transcriptome/mRNA set, CleaveLand outputs potentially cleaved small RNA targets along with other supporting information.
::DEVELOPER
Axtell Lab @ Penn State
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Addo-Quaye, C., Miller, W., and Axtell, M.J. (2009).
CleaveLand: A pipeline for using degradome data to find cleaved small RNA targets.
Bioinformatics 25: 130-131.
:: DESCRIPTION
PatternBranching and ProfileBranching are softwares for finding subtle motifs by branching from sample strings
::DEVELOPER
Alkes Price , Sriram Ramabhadran and Pavel A. Pevzner
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Price A., Ramabhadran S., Pevzner P.A. 2003.
Finding subtle motifs by branching from sample strings.
Bioinformatics. 2003 Oct;19 Suppl 2:ii149-55.
:: DESCRIPTION
FIND is a software package designed to facilitate the visualization and analysis of Flow Cytometry data for the scientific target audience, as well as providing a target platform for developers to implement their FC-specific algorithms.
::DEVELOPER
Battelle Center for Mathematical Medicine
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2011 May 10;12:145. doi: 10.1186/1471-2105-12-145.
FIND: a new software tool and development platform for enhanced multicolor flow analysis.
Dabdoub SM1, Ray WC, Justice SS.
:: DESCRIPTION
GoFish selects a subset of Gene Ontology (GO) attributes, and ranks genes according to the probability of having all those attributes.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2003 Apr 12;19(6):788-9.
GoFish finds genes with combinations of Gene Ontology attributes.
Berriz GF, White JV, King OD, Roth FP.
:: DESCRIPTION
SnowShoes-FTD is a bioinformatics tool to identify fusion transcripts from paired-end transcriptome sequencing data. The tool employs multiple steps of false positive filtering and nominates the fusion candidates with high confidence (approaching 100% true positive rate). The unique features of SnowShoes-FTD include: (i) the ability to discover multiple fusion isoforms in which the two gene partners give rise to transcripts with different junctions; (ii) prediction of potential fusion mechanisms including inversion, translocation, and/or interstitial deletions; (iii) identification of whether the junction point in a fusion transcript occurs at the boundaries of known exons which implies the fusion events might have happened inside an intron in DNA and transcribed to the fusion transcript.
::DEVELOPER
Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Nucleic Acids Res. 2011 Aug;39(15):e100. Epub 2011 May 27.
A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines.
Asmann YW, Hossain A, Necela BM, Middha S, Kalari KR, Sun Z, Chai HS, Williamson DW, Radisky D, Schroth GP, Kocher JP, Perez EA, Thompson EA.
:: DESCRIPTION
FOOTER analyses a pair of homologous mammalian DNA sequences (i.e. human and mouse/rat) for high probability binding sites of known transcription factors. A set of Position-Specific Scoring Matrices (PSSM) has been carefully constructed from mammalian transcription factor binding sites deposited in TRANSFAC database.
::DEVELOPER
SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting.
Corcoran DL, Feingold E, Benos PV.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W442-6.
:: DESCRIPTION
PhiSpy is a novel algorithm for finding prophages in microbial genomes that combines similarity-based and composition-based strategies
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2012 Sep;40(16):e126. doi: 10.1093/nar/gks406. Epub 2012 May 14.
PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies.
Akhter S1, Aziz RK, Edwards RA.
:: DESCRIPTION
LBL (Logistic Bayesian Lasso) is an R package that performs Logistic Bayesian Lasso for finding association of SNP haplotypes with a trait in a case-control setting. Bayesian lasso is used to find the posterior distributions of logistic regression coefficients, which are then used to calculate Bayes Factor to test for association with haplotypes.
LBLGXE expands on the original LBL. Gene-environment interaction (GXE)
::DEVELOPER
Statistical Genetics and Bioinformatics Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genet Epidemiol. 2014 Jan;38(1):31-41. doi: 10.1002/gepi.21773. Epub 2013 Nov 23.
Detecting rare haplotype-environment interaction with logistic Bayesian LASSO.
Biswas S1, Xia S, Lin S.
Biswas S, and Lin, S. (2011)
Logistic Bayesian Lasso for identifying association with rare haplotyp es and application to age-related macular degeneration.
Biometrics. 2011 Sep 28. doi: 10.1111/j.1541-0420.
