Tag: Frequency

SLPFA – Subcellular Location Prediction with Frequency and Alignment

SLPFA

:: DESCRIPTION

SLPFA is a predictor for subcellular location prediction of proteins by feature vectors based on amino acid composition (frequency) and sequence alignment. 90.96% of overall accuracy was obtained through fivefold cross validation tests with TargetP plant data sets.

SLPFA is an improved subcellular location predictor of SLP-Local

::DEVELOPER

Akutsu Laboratory (Laboratory of Mathematical Bioinformatics)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2007 Nov 30;8:466.
Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition.
Tamura T, Akutsu T.

FreClu – Efficient Frequency-based De novo Short Read Clustering

FreClu

:: DESCRIPTION

FreClu: Efficient Frequency-based De novo Short Read Clustering — de novo clustering

::DEVELOPER

Morishita Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java 

:: DOWNLOAD

 FreClu

:: MORE INFORMATION

Citation

Wei Qu, Shin-ichi Hashimoto and Shinichi Morishita
Efficient frequency-based de novo short read clustering for error trimming in next-generation sequencing.
Genome Res. 2009. 19:1309-1315

 

IBDseq – Detect IBD Segments using Allele Frequencies

IBDseq

:: DESCRIPTION

IBDseq is a software program for detecting segments of identity-by-descent (IBD) and homozygosity-by-descent (HBD) in unphased genetic sequence data.

::DEVELOPER

Brian L. Browning 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

IBDseq

:: MORE INFORMATION

Citation:

Browning BL, Browning SR.
Detecting identity by descent and estimating genotype error rates in sequence data.
Am J Hum Genet. 2013 Nov 7;93(5):840-51. doi: 10.1016/j.ajhg.2013.09.014. Epub 2013 Oct 24. PMID: 24207118; PMCID: PMC3824133.

KCOSS 2021 – A K-mer Frequency Statistics Software

KCOSS 2021

:: DESCRIPTION

KCOSS is used to count the sequence files in FASTA format and save the statistical results as binary files to save space.

::DEVELOPER

KCOSS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

KCOSS

:: MORE INFORMATION

Citation:

Tang D, Li Y, Tan D, Fu J, Tang Y, Lin J, Zhao R, Du H, Zhao Z.
KCOSS: an ultra-fast k-mer counter for assembled genome analysis.
Bioinformatics. 2021 Nov 26:btab797. doi: 10.1093/bioinformatics/btab797. Epub ahead of print. PMID: 34849595.

allelefreq – Bayes Allele Frequency Software

allelefreq

:: DESCRIPTION

allelefreq calculates estimated allele frequencies based on actual frequencies.

::DEVELOPER

The Devlin lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • C Compiler

:: DOWNLOAD

  allelefreq

:: MORE INFORMATION

Citation:

Lockwood et al, 2001,
A Bayesian hierarchical model for allele frequencies
Genetic Epidemiology 20:17-33

Ehapp – Estimate Haplotype Frequency from Pooled Sequencing data

Ehapp

:: DESCRIPTION

Taking advantage of prior haplotype database, Ehapp implements lsqnonneg and GPSR algrithm to estimate the frequencies of haplotypes from pooled sequencing data.

::DEVELOPER

Bioinfomatics Lab of SouthEast Universtity

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 Ehapp

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Oct 9. pii: btu670.
Accurate estimation of haplotype frequency from pooled sequencing data and cost-effective identification of rare haplotype carriers by overlapping pool sequencing.
Cao CC1, Sun X

d2SBin v1.0 – Improving the Binning of Metagenomic Contigs on d2S Oligonucleotide Frequency Dissimilarity

d2SBin v1.0

:: DESCRIPTION

d2SBin is easy-to-use contig-binning improving tool, which adjusted the contigs among bins based on the output of any existing binning tools. The tool is taxonomy-free only on the k-tuples for single metagenomic sample.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Python

:: DOWNLOAD

d2SBin

:: MORE INFORMATION

Citation

Wang Y, Wang K, Lu YY, Sun F.
Improving contig binning of metagenomic data using [Formula: see text] oligonucleotide frequency dissimilarity.
BMC Bioinformatics. 2017 Sep 20;18(1):425. doi: 10.1186/s12859-017-1835-1. PMID: 28931373; PMCID: PMC5607646.

SFselect – Learning Natural Selection from the Site Frequency Spectrum

SFselect

:: DESCRIPTION

SFselect is a method for classifying genomic regions evolving under positive selection, from those evolving neutrally

::DEVELOPER

Roy Ronen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SFselect

:: MORE INFORMATION

Citation

Genetics. 2013 Sep;195(1):181-93. doi: 10.1534/genetics.113.152587. Epub 2013 Jun 14.
Learning natural selection from the site frequency spectrum.
Ronen R, Udpa N, Halperin E, Bafna V.

SNPHAP 1.3.1 – Estimate Frequencies of Haplotypes of SNPs

SNPHAP 1.3.1

:: DESCRIPTION

SNPHAP is a program for estimating frequencies of haplotypes of large numbers of diallelic markers from unphased genotype data from unrelated subjects

::DEVELOPER

David Clayton (david.clayton@cimr.cam.ac.uk)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/WIndows
  • C Compiler

:: DOWNLOAD

  SNPHAP

:: MORE INFORMATION

CoNVEM – CNV Allele Frequency Estimation by Expectation Maximisation

CoNVEM

:: DESCRIPTION

CoNVEM (Copy Number Variation Expectation Maximisation) is an expectation-maximization program for determining allelic spectrum from CNV data (CoNVEM)

::DEVELOPER

Tom Gaunt’s group in the MRC IEU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Hum Mutat. 2010 Apr;31(4):414-20. doi: 10.1002/humu.21199.
An expectation-maximization program for determining allelic spectrum from CNV data (CoNVEM): insights into population allelic architecture and its mutational history.
Gaunt TR1, Rodriguez S, Guthrie PA, Day IN.