Tag: Identifying

CrypticIBDcheck 0.3-3 – Identifying Cryptic Relatedness in Genetic Association Studies

CrypticIBDcheck 0.3-3

:: DESCRIPTION

CrypticIBDcheck can be used to identify pairs of closely-related subjects based on genetic marker data from single-nucleotide polymorphisms (SNPs). The package is able to accommodate SNPs in linkage disequibrium (LD), without the need to thin the markers so that they are approximately independent in the population. Sample pairs are identified as related by superposing their estimated identity-by-descent (IBD) coefficients on plots of IBD coefficients for pairs of simulated subjects from one of several common close relationships.

::DEVELOPER

Graham & McNeney Labs

: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CrypticIBDcheck

:: MORE INFORMATION

Citation

Source Code Biol Med. 2013 Feb 6;8(1):5. doi: 10.1186/1751-0473-8-5.
CrypticIBDcheck: an R package for checking cryptic relatedness in nominally unrelated individuals.
Nembot-Simo A, Graham J, McNeney B.

GeneCOST – Identifying Disease causing Genes

GeneCOST

:: DESCRIPTION

GeneCOST is a novel scoring based method to evaluate every gene for its disease association.

::DEVELOPER

Advanced Genomics and Bioinformatic Research Group, İGBAM

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

GeneCOST

:: MORE INFORMATION

Citation

Ozer B, Sağıroğlu M, Demirci H.
GeneCOST: a novel scoring-based prioritization framework for identifying disease causing genes.
Bioinformatics. 2015 Nov 15;31(22):3715-7. doi: 10.1093/bioinformatics/btv424. Epub 2015 Jul 21. PMID: 26203168.

Partition 2.0 / PartitionML / PartitionView – maximum likelihood / Identifying Population Sub-division & Assigning Individuals to Populations

Partition 2.0 / PartitionML / PartitionView

:: DESCRIPTION

Partition is a model-based statistical software package for identifying population sub-division and assigning individuals to populations, on the basis of their genotypes at co-dominant marker loci. The underlying population genetic model is appropriate for out-crossing diploid organisms.

PartitionML is a program that searches for the best possible partition of a sample into independent panmictic clusters and simultaneously assign individuals to them using a maximum likelihood (ML) criterion.

PartitionView will read the  partition output file, as it is being written, and will display the path of the Markov chain (see below) as it evolves in real time.

::DEVELOPER

Partition team

:: SCREENSHOTS

Partition

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Partition  / PartitionML

:: MORE INFORMATION

Citation

Heredity (Edinb). 2009 Jul;103(1):32-45. doi: 10.1038/hdy.2009.29. Epub 2009 Apr 1.
An agglomerative hierarchical approach to visualization in Bayesian clustering problems.
Dawson KJ1, Belkhir K.

Heredity (Edinb). 2002 Jul;89(1):27-35.
Heterozygote deficiencies in small lacustrine populations of brook charr Salvelinus Fontinalis Mitchill (Pisces, Salmonidae): a test of alternative hypotheses.
Castric V1, Bernatchez L, Belkhir K, Bonhomme F.

ellipsoidFN 0.0.1 – Identifying a Heterogeneous set of Cancer Biomarkers based on Gene Expressions

ellipsoidFN 0.0.1

:: DESCRIPTION

ellipsoidFN (ellipsoid Feature Net) is a software to model the disease complexity by ellipsoids and seek a set of heterogeneous biomarkers.

::DEVELOPER

APORC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux /MacOsX
  • matlab

:: DOWNLOAD

 ellipsoidFN

:: MORE INFORMATION

Citation

Xianwen Ren, Yong Wang, Luonan Chen, Xiang-Sun Zhang, and Qi Jin.
ellipsoidFN: a tool for identifying a heterogeneous set of cancer biomarkers based on gene expressions.
Nucleic Acids Research, 2013 41: e53.

HMMCAS – Identifying Cas Genes and Proteins

HMMCAS

:: DESCRIPTION

HMMCAS is a program to identify Cas proteins in archaea and bacteria proteome. You can also use this web tool to find Cas proteins in your interested proteome such as giant virus.

::DEVELOPER

HLAB: Huang’s LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Chai G, Yu M, Jiang L, Duan Y, Huang J.
HMMCAS: A Web Tool for the Identification and Domain Annotations of CAS Proteins.
IEEE/ACM Trans Comput Biol Bioinform. 2019 Jul-Aug;16(4):1313-1315. doi: 10.1109/TCBB.2017.2665542. Epub 2017 Feb 7. PMID: 28186905.

segmentSeq 2.26.0 – Identifying small RNA loci from High-throughput Sequencing data

segmentSeq 2.26.0

:: DESCRIPTION

segmentSeq is a methods for identifying small RNA loci from high-throughput sequencing data

::DEVELOPER

Thomas J. Hardcastle

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 segmentSeq

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Feb 15;28(4):457-63. doi: 10.1093/bioinformatics/btr687. Epub 2011 Dec 9.
Identifying small interfering RNA loci from high-throughput sequencing data.
Hardcastle TJ, Kelly KA, Baulcombe DC.

ChIPseqR 1.46.0 – Identifying Protein Binding Sites in High-Throughput Sequencing Data

ChIPseqR 1.46.0

:: DESCRIPTION

ChIPseqR is an algorithm for the analysis of nucleosome positioning and histone modification ChIP-seq experiments.

::DEVELOPER

CSIRO Transformational Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 ChIPseqR

:: MORE INFORMATION

Citation

ChIPseqR: analysis of ChIP-seq experiments.
Humburg P, Helliwell CA, Bulger D, Stone G.
BMC Bioinformatics. 2011 Jan 31;12:39. doi: 10.1186/1471-2105-12-39.

AgileAnnotator 20140613 – Identifying Sequence Variants in ordered SAM files

AgileAnnotator 20140613

:: DESCRIPTION

AgileAnnotator identifies sequence variants that repeatedly occur in reads that have previously been aligned to a reference sequence by an alignment program, such as BWA or Novoalign, and exported as SAM files.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0 

:: DOWNLOAD

 AgileAnnotator

:: MORE INFORMATION

VIRS – A Visual tool for Identifying Restriction Sites

VIRS

:: DESCRIPTION

VIRS is an interactive web-based program designed for restriction endonuclease cut sites prediction and visualisation. The system permits to simultaneously process batch DNA sequences, and produces visual restriction maps with several useful options for users’ customisation. These options also perform in-depth analysis of the restriction maps, such as virtual electrophoretic result for digested fragments. Different from other analytical tools, VIRS not only displays visual outputs, but also provides the detailed properties of enzymes that are commercially avaialbe. All the information correlates with enzymes is stored in our database, which is updated monthly from the manufacturers’ websites.

::DEVELOPER

BIS @ Zhejiang University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Xiang Chen, Cong Luo, Xiaoxia Ma, Ming Chen* (2009)
VIRS: a visual tool for identifying restriction sites in multiple DNA sequences.
Biotechnology Progress, 25(5): 1525-1527.

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