:: DESCRIPTION
FlaiMapper is a method that extracts and annotates the locations of sncRNA-derived RNAs (sncdRNAs).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Oct 22. pii: btu696.
FlaiMapper: computational annotation of small ncRNA derived fragments using RNA-seq high throughput data.
Hoogstrate Y, Jenster G, Martens-Uzunova ES
:: DESCRIPTION
HiSIF is a novel computational software tool on Hi-C data analysis, including a Poisson Mixture Model, with an Expectation Maximization algorithm (EM) followed by a power-law decay background model to filter background-ligation events.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhou Y, Cheng X, Yang Y, Li T, Li J, Huang TH, Wang J, Lin S, Jin VX.
Modeling and analysis of Hi-C data by HiSIF identifies characteristic promoter-distal loops.
Genome Med. 2020 Aug 12;12(1):69. doi: 10.1186/s13073-020-00769-8. PMID: 32787954; PMCID: PMC7425017.
:: DESCRIPTION
MINTbase: a web-based framework that serves the dual-purpose of being a content repository for tRFs and a tool for the interactive exploration of these newly discovered molecules.
::DEVELOPER
the Computational Medicine Center at the Sidney Kimmel Medical College of Thomas Jefferson University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Pliatsika, V, Loher, P, Telonis, AG, Rigoutsos, I.
MINTbase: a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments
Bioinformatics. 2016; In press.
:: DESCRIPTION
Megraft is a software package that grafts SSU (small subunit) fragments onto full-length SSU sequences, accounting for observed and unobserved variability, for accurate assessment of species richness and sequencing depth in metagenomics endeavors.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Res Microbiol. 2012 Jul;163(6-7):407-12. doi: 10.1016/j.resmic.2012.07.001. Epub 2012 Jul 21.
Megraft: a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets.
Bengtsson J, Hartmann M, Unterseher M, Vaishampayan P, Abarenkov K, Durso L, Bik EM, Garey JR, Eriksson KM, Nilsson R
:: DESCRIPTION
FCP (Fragment classification package) is a homology- and composition-based classifiers for assigning a taxonomic attribution to metagenomic fragments.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Parks, D.H., MacDonald, N.J., and Beiko, R.G. (2011).
Classifying short genomic fragments from novel lineages using composition and homology.
BMC Bioinformatics, 12:328.
:: DESCRIPTION
FSDA is an alternative framework for identifying sub-chromosomal copy number variations in a fetal genome.
:: DEVELOPER
Computational Biology Lab at the University of Toronto
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Cell-free DNA fragment-size distribution analysis for non-invasive prenatal CNV prediction.
Arbabi A, Rampášek L, Brudno M.
Bioinformatics. 2016 Apr 5. pii: btw178.
:: DESCRIPTION
FRAGSION is a database-free method to efficiently generate protein fragment library by sampling from an Input-Output Hidden Markov Model.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling.
Bhattacharya D, Adhikari B, Li J, Cheng J.
Bioinformatics. 2016 Feb 18. pii: btw067
:: DESCRIPTION
cBar is a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data
::DEVELOPER
the Computational Systems Biology Laboratory at the University of Georgia
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Fengfeng Zhou, Ying Xu
cBar: a computer program to distinguish plasmid-derived from chromosome-derived sequence fragments in metagenomics data
Bioinformatics, 2010 26(16):2051-2052.
:: DESCRIPTION
FESTA (Fragmented Exhaustive Search for TAgSNPs) selects tagSNPs based on the pairwise LD measure r2. Using a pre-specified threshold d, it generates a tagSNP set such that every SNP is either in the tagSNP set itself or is in LD (with r2 > d ) with at least one SNP in the tagSNP set. This is an extension of the greedy approach proposed in Carlson et al. (2004). The basic idea is to partition the whole SNP set into disjoint precincts. Including or excluding certain SNPs, requiring double coverage of SNPs, as well as the original greedy approach (on disjoint precincts) are also included in this package.
::DEVELOPER
Shyam Gopalakrishnan (gopalakr@umich.edu), Steve Qin @ the Center for Statistical Genetics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Qin ZS, Gopalakrishnan S, Abecasis G
An effcient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria.
Bioinformatics (2006) 22 (2): 220-225.
