Tag: Detect

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.

Ringer – Detect Molecular Motions by automatic Electron Density Sampling

Ringer

:: DESCRIPTION

The program Ringer detects molecular motions by automatic electron density sampling. The aim of Ringer is to go beyond static structural snapshots of proteins by uncovering structural ensembles in X-ray electron density. This information can reveal not only which parts of proteins are flexible and which part are rigid, but it also can define alternate conformations that may be important for function. Alternate conformations of binding sites also may afford additional targets for drug design.

::DEVELOPER

Alber Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 Ringer

:: MORE INFORMATION

Citation

Lang et al.
Automated electron-density sampling reveals widespread conformational polymorphism in proteins.
Protein Sci.: 2010, 19(7);1420-31.

PathSeq 2.0 – Detect Pathogenic Sequences

PathSeq 2.0

:: DESCRIPTION

PathSeq is a computational tool for the identification and analysis of microbial sequences in high-throughput human sequencing data that is designed to work with large numbers of sequencing reads in a scalable manner. This process is composed of a subtractive phase in which input reads are subtracted by alignment to human reference sequences, and an analytic phase in which the remaining reads are aligned to microbial reference sequences (viral, fungal, bacterial, archaeal) and de novo assembled.

::DEVELOPER

The Cancer Genome Analysis (CGA) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PathSeq

:: MORE INFORMATION

Citation

Nat Biotechnol. 2011 May;29(5):393-6.
PathSeq: software to identify or discover microbes by deep sequencing of human tissue.
Kostic AD, Ojesina AI, Pedamallu CS, Jung J, Verhaak RG, Getz G, Meyerson M.

Chimerascan 0.4.5a – Detect Gene Fusions in Paired-end RNA Sequencing (RNA-Seq) Datasets

Chimerascan 0.4.5a

:: DESCRIPTION

Chimerascan is a  software for detecting gene fusions in paired-end RNA sequencing (RNA-Seq) datasets.

::DEVELOPER

The Michigan Center for Translational Pathology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Chimerascan

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Oct 15;27(20):2903-4. Epub 2011 Aug 11.
ChimeraScan: a tool for identifying chimeric transcription in sequencing data.
Iyer MK, Chinnaiyan AM, Maher CA.

PCAdapt 201405 – Detect Genes Targetted by Selection

PCAdapt 201405

:: DESCRIPTION

PCAdapt is a software to detect footprints of local adaptation in population genetics data set.

::DEVELOPER

Nicolas Duforet-Frebourg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • C Compiler

:: DOWNLOAD

 PCAdapt

:: MORE INFORMATION

Citation

Mol Biol Evol. 2014 Jun 3. pii: msu182. [Epub ahead of print]
Genome scans for detecting footprints of local adaptation using a Bayesian factor model.
Duforet-Frebourg N1, Bazin E2, Blum MG3.

RepWords 1.1 – Detect Tandem Repeats in FASTA Sequences

RepWords 1.1

:: DESCRIPTION

RepWords detects tandem repeats in FASTA sequences.

::DEVELOPER

Statistical Computational Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • C++ Compiler

:: DOWNLOAD

 RepWords

:: MORE INFORMATION

Citation

Int J Bioinform Res Appl. 2014;10(4):384-408. doi: 10.1504/IJBRA.2014.062991.
Searching for repeats, as an example of using the generalised Ruzzo-Tompa algorithm to find optimal subsequences with gaps.
Spouge JL, Mariño-Ramírez L, Sheetlin SL.

Redeem 1.1 – Detect Sequencing Errors in Illumina reads

Redeem 1.1

:: DESCRIPTION

Redeem (Read error detection in repetitive genomes)detects sequencing errors in Illumina reads (might be applicable for other types of next-gen sequencing equipments).

::DEVELOPER

Prof. Srinivas Aluru Research group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 Redeem

:: MORE INFORMATION

Citation

X. Yang, S. Aluru and K. Dorman,
“Repeat-aware Modeling and Correction of Short Read Errors”,
BMC Bioinformatics, 2011 to appear.

FusionAnalyser – Detect Gene Fusions from paired-end RNA-Seq data

FusionAnalyser

:: DESCRIPTION

FusionAnalyser is a software for detecting gene fusions from paired-end RNA-Seq data.FusionAnalyser uses paired reads mapping to different genes (Bridge reads),  generated through high-throughput whole transcriptome sequencing, to build a first dataset of candidate fusion events. Subsequently, a second dataset, built upon those reads where only one of the two sequences in a pair is successfully mapped to the reference genome (‘Half-mapped Anchor reads’), is generated. The mapped reads in the latter dataset are used as an anchor to tie each Half-mapped event to the corresponding Bridge region.

::DEVELOPER

Rocco Piazza 

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / WIndows

:: DOWNLOAD

 FusionAnalyser 

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2012 Sep 1;40(16):e123. Epub 2012 May 8.
FusionAnalyser: a new graphical, event-driven tool for fusion rearrangements discovery.
Piazza R, Pirola A, Spinelli R, Valletta S, Redaelli S, Magistroni V, Gambacorti-Passerini C.

GISTIC 2.0.23 – Detect Regions of Significant Copy-number Gains and Losses

GISTIC 2.0.23

:: DESCRIPTION

GISTIC  (Genomic Identification of Significant Targets in Cancer) facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

::DEVELOPER

The Cancer Genome Analysis (CGA) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GISTIC

:: MORE INFORMATION

Citation

Genome Biol. 2011;12(4):R41. Epub 2011 Apr 28.
GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers.
Mermel CH, Schumacher SE, Hill B, Meyerson ML, Beroukhim R, Getz G.

CDS-plotcon – Detect Enhanced Conservation in Coding Sequences

CDS-plotcon

:: DESCRIPTION

The software package CDS-plotcon is specifically designed to search for conserved functional elements within CDSs. It uses an average model of the expected mutation patterns within CDSs (incorporating a nucleotide mutation matrix, amino acid substitution matrix, sequence divergence parameter t, mean synonymous:nonsynonymous substitution ratio V and phylogenetic tree; it can handle up to three overlapping CDSs in different read-frames). Using this, it calculates the expected number of mutations across the alignment in each column and compares this with the observed number of mutations. The results are plotted along the genome, and optionally passed through a sliding window (clipped) mean filter

::DEVELOPER

Andrew Firth

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 CDS-plotcon

:: MORE INFORMATION

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