FRAGSION 1.0 – Protein Fragment Library Generation

FRAGSION 1.0

:: DESCRIPTION

FRAGSION is a database-free method to efficiently generate protein fragment library by sampling from an Input-Output Hidden Markov Model.

::DEVELOPER

Dr. Jianlin Cheng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 FRAGSION

:: 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

FSDA – Fragment Size Distribution Analysis for non-invasive prenatal CNV prediction

FSDA

:: 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

  • Linux

:: DOWNLOAD

 FSDA

:: 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.

FCP 1.0.7 – Fragment Classification Package

FCP 1.0.7

:: DESCRIPTION

FCP (Fragment classification package) is a homology- and composition-based classifiers for assigning a taxonomic attribution to metagenomic fragments.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

 FCP

:: 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.

MINTbase – Exploration of Mitochondrial and Nuclear tRNA Fragments

MINTbase

:: 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

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

MINTplates

:: 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.

FlaiMapper 1.2.0 – Fragment Location Annotation Identification Mapper

FlaiMapper 1.2.0

:: DESCRIPTION

FlaiMapper is a method that extracts and annotates the locations of sncRNA-derived RNAs (sncdRNAs).

::DEVELOPER

FlaiMapper team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FlaiMapper

:: 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

RNAfbinv – Fragment-Based Design of RNA sequences

RNAfbinv

:: DESCRIPTION

RNAfbinv is an interactive java application that performs RNA sequence design, constrained to yield a specific RNA shape and physical attributes.

::DEVELOPER

RNAfbinv team

:: SCREENSHOTS

RNAfbinv

:: REQUIREMENTS

  • Windows/Linux
  • JRE

:: DOWNLOAD

RNAfbinv

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Nov 15;29(22):2938-40. doi: 10.1093/bioinformatics/btt494. Epub 2013 Aug 23.
RNAfbinv: an interactive Java application for fragment-based design of RNA sequences.
Weinbrand L1, Avihoo A, Barash D.

Fragment Merger Tool – Merge Overlapping Long Sequence Fragments

Fragment Merger Tool

:: DESCRIPTION

The Fragment Merger Tool produces a single (merged) sequence from two to twelve overlapping input fragments. These fragments can be chromatograms (ABIF files in .ab1 format) or FASTA files, or a mixture of both.

::DEVELOPER

Dr Trevor Bell [Trevor.Bell (@) wits.ac.za]

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Bell, T. G. and Kramvis, A. (2013)
Fragment Merger: An online tool to merge overlapping long sequence fragments.
Viruses 5: 824-833.

Megraft 1.0.2 – Graft Ribosomal Small Subunit (16S/18S) Fragments onto full-length SSU Sequences

Megraft 1.0.2

:: 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

Johan Bengtsson

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 Megraft

:: 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

cBar 1.2 – Identification of Chromosomal Sequence Fragments from Metagenome data

cBar 1.2

:: 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

 cBar

:: 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.

FESTA 2.0 – Fragmented Exhaustive Search for TAgSNPs

FESTA 2.0

:: 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

  • Linux / MacOsX

:: DOWNLOAD

 FESTA

:: 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.