diCal 1.3 / diCal-IBD 1.0 – Predicts Identical by Descent Tracts using Sequence data

diCal 1.3 / diCal-IBD 1.0

:: DESCRIPTION

diCal is a scalable demographic inference method based on the sequentially Markov conditional sampling distribution framework.

diCal-IBD can be used for predicting identical by descent (IBD) tracts in sequence data. It provides means for calculating the accuracy of the prediction, if the true tracts are available, plotting of the predicted tracts, their TMRCA (time to the most recent common ancestor) and corresponding posterior probabilities, and identification of putative recent positive selection through investigation of average IBD sharing

::DEVELOPER

The Biophysics Graduate Group, Yun S. Song

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Python

:: DOWNLOAD

  diCal-IBD , diCal

:: MORE INFORMATION

Citation

Genetics. 2013 Jul;194(3):647-62. doi: 10.1534/genetics.112.149096. Epub 2013 Apr 22.
Estimating variable effective population sizes from multiple genomes: a sequentially markov conditional sampling distribution approach.
Sheehan S1, Harris K, Song YS.

diCal-IBD: demography-aware inference of identity-by-descent tracts in unrelated individuals.
Tataru P, Nirody JA, Song YS.
Bioinformatics. 2014 Aug 21. pii: btu563

PRINSEQ 0.20.4 – Preprocess and Generate Statistics about Sequence data

PRINSEQ 0.20.4

:: DESCRIPTION

PRINSEQ (PReprocessing and INformation of SEQuence data.) is a tool that generates summary statistics of sequence and quality data and that is used to filter, reformat and trim next-generation sequence data. It is particular designed for 454/Roche data, but can also be used for other types of sequence data. PRINSEQ is available through a user-friendly web interface or as standalone version. The standalone version is primarily designed for data preprocessing and does not generate summary statistics in graphical form.

PRINSEQ Online Version

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX / Linux /
  • Perl

:: DOWNLOAD

 PRINSEQ

:: MORE INFORMATION

Citation:

Schmieder R and Edwards R
Quality control and preprocessing of metagenomic datasets.
Bioinformatics 2011, 27:863-864.

SpliceSeq 2.1 – Investigate alternative mRNA Splicing in Next Generation mRNA Sequence data

SpliceSeq 2.1

:: DESCRIPTION

SpliceSeq provides a quick, easy method of investigating alternative mRNA splicing in next generation mRNA sequence data. The tool may be used on a single mRNA-Seq sample to identify genes with multiple spliceforms or on a pair of samples to identify differential splicing between the samples. Sequence reads are mapped to splice graphs that unambiguously quantify the inclusion level of each exon and splice junction. The graphs are then traversed to predict the protein isoforms that are likely to result from the observed exon and splice junction reads. UniProt annotations are mapped to each protein isoform to identify potential functional impacts of alternative splicing.

::DEVELOPER

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 SpliceSeq

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 15;28(18):2385-7. Epub 2012 Jul 20.
SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts.
Ryan MC, Cleland J, Kim R, Wong WC, Weinstein JN.

SEQMINER 4.9 – Efficiently Read Sequence Data into R

SEQMINER 4.9

:: DESCRIPTION

SEQMINER is an R package for annotating and querying files of sequence variants (e.g., VCF/BCF files) and summary association statistics (e.g., METAL/RAREMETAL files), and for integrating bioinformatics databases.

::DEVELOPER

SEQMINER team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 SEQMINER

:: MORE INFORMATION

Citation

SEQMINER: An R-Package to Facilitate the Functional Interpretation of Sequence-Based Associations.
Zhan X, Liu DJ.
Genet Epidemiol. 2015 Sep 23. doi: 10.1002/gepi.21918.

ASAP 1.1.7 – Automated Sequence data Processing on Computer Clusters

ASAP 1.1.7

:: DESCRIPTION

ASAP (Advanced Sequence Automated Pipeline)is an open source pipeline designed to assist users in managing various jobs associated with processing HiSeq data on a cluster or in serial. . The software was designed to alleviate these issues by providing a modular system to allow users with different needs to process their data with a minimal amount of effort. In addition to minimizing human involvement, ASAP is designed to work on the researcher’s local computer cluster, if one is available

::DEVELOPER

Chun Li, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  ASAP

:: MORE INFORMATION

Citation

BMC Res Notes. 2013 Jan 4;6:5. doi: 10.1186/1756-0500-6-5.
ASAP: an environment for automated preprocessing of sequencing data.
Torstenson ES1, Li B, Li C.

SeqPop – Compute Population Genetics Statistics on Sequence Data

SeqPop

:: DESCRIPTION

SeqPop is a program for computing population genetics statistics on sequence data, including Pn, Theta, Pi(i,j), Kst(*), Fst(*), and their Monte Carlo significance for population subdivision.

::DEVELOPER

the Townsend Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac

:: DOWNLOAD

  SeqPop

:: MORE INFORMATION

BM-BC 1.0 – Bayesian method of Base Calling for Solexa Sequence data

BM-BC 1.0

:: DESCRIPTION

BM-BC is a Bayesian method of base calling for Solexa-GA sequencing data. The Bayesian method builds on a hierarchical model that accounts for three sources of noise in the data, which are known to affect the accuracy of the base calls: fading, phasing, and cross-talk between channels.

::DEVELOPER

Yuan Ji Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package

:: DOWNLOAD

 BM-BC

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012;13 Suppl 13:S6. doi: 10.1186/1471-2105-13-S13-S6. Epub 2012 Aug 24.
BM-BC: a Bayesian method of base calling for Solexa sequence data.
Ji Y, Mitra R, Quintana F, Jara A, Mueller P, Liu P, Lu Y, Liang S.

Hapler 1.60 – Haplotype Phasing of Population-sourced Sequence data

Hapler 1.60

:: DESCRIPTION

Hapler is a tool for assembling robust haplotype regions given alignments (from de-novo assembly or mapping to a reference) of genetically diverse sequence data. Hapler compares each sequence to every other, and groups sequences together into sets that don’t have any conflicts (minimum coloring of the sequence ‘conflict graph’). This can be done in O(n^3) time, because Hapler assumes that sequences contain no gaps (e.g., it ignores mate-pair information). Because such a minimum coloring is usually not unique, Hapler by default produces many pseudo-random colorings and only keeps haplotype groupings which are common to all. In practice this drastically increases the correctness of results.

::DEVELOPER

ND Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

  Hapler

:: MORE INFORMATION

Citation

BMC Genomics. 2012 Apr 12;13 Suppl 2:S4. doi: 10.1186/1471-2164-13-S2-S4.
Haplotype and minimum-chimerism consensus determination using short sequence data.
O’Neil ST, Emrich SJ.

scan-x 1.1 – Find Motifs within any Sequence data set

scan-x 1.1

:: DESCRIPTION

scan-x is a software tool designed to find motifs within any sequence data set. The first large scale scan was performed using all available human, mouse, fly and yeast phosphorylation and acetylation data to perform a scan for undiscovered modification sites.

::DEVELOPER

Schwartz Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Mol Cell Proteomics. 2009 Feb;8(2):365-79. doi: 10.1074/mcp.M800332-MCP200. Epub 2008 Oct 28.
Predicting protein post-translational modifications using meta-analysis of proteome scale data sets.
Schwartz D, Chou MF, Church GM.

Curr Protoc Bioinformatics. 2011 Dec;Chapter 13:Unit 13.16.. doi: 10.1002/0471250953.bi1316s36.
Using the scan-x Web site to predict protein post-translational modifications.
Chou MF, Schwartz D.

CS23D 2.0 – Protein Structure generation using NMR Chemical Shifts and Sequence data

CS23D 2.0

:: DESCRIPTION

CS23D (Chemical Shift to 3D Structure) is a web server for rapidly generating accurate 3D protein structures using only assigned NMR chemical shifts as input.

::DEVELOPER

the Wishart Research Group, University of Alberta

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W496-502. doi: 10.1093/nar/gkn305. Epub 2008 May 30.
CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data.
Wishart DS, Arndt D, Berjanskii M, Tang P, Zhou J, Lin G.