ReliefSeq – Ranking Features of Genetic Sequence data using Relief-F

ReliefSeq

:: DESCRIPTION

ReliefSeq is a feature (attribute) selection and ranking algorithm written in C++ designed to handle various types of genetic features including combinations of feature data types and endpoints (phenotypes/classes).

::DEVELOPER

Insilico Research Group (McKinney Laboratory for Bioinformatics and In Silico Modeling)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

ReliefSeq

:: MORE INFORMATION

Citation

PLoS One. 2013 Dec 10;8(12):e81527. doi: 10.1371/journal.pone.0081527. eCollection 2013.
ReliefSeq: a gene-wise adaptive-K nearest-neighbor feature selection tool for finding gene-gene interactions and main effects in mRNA-Seq gene expression data.
McKinney BA, White BC, Grill DE, Li PW, Kennedy RB, Poland GA, Oberg AL.

vt 0.57721 – A tool set for Short Variant Discovery in Genetic Sequence Data

vt 0.57721

:: DESCRIPTION

vt is a variant tool set that discovers short variants from Next Generation Sequencing data.

::DEVELOPER

Adrian Tan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Unified Representation of Genetic Variants.
Tan A, Abecasis GR, Kang HM.
Bioinformatics. 2015 Feb 19. pii: btv112.

SA-SSR – A Novel Algorithm for SSR Discovery in Genetic Sequences

SA-SSR

:: DESCRIPTION

SA-SSR is a software tool developed to find Simple Sequence Repeats (SSRs) in a sequence (presumably of DNA or RNA).

::DEVELOPER

Perry Ridge Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

SA-SSR

:: MORE INFORMATION

Citation

SA-SSR: A Suffix Array-Based Algorithm for Exhaustive and Efficient SSR Discovery in Large Genetic Sequences.
Pickett BD, Karlinsey SM, Penrod CE, Cormier MJ, Ebbert MT, Shiozawa DK, Whipple CJ, Ridge PG.
Bioinformatics. 2016 May 11. pii: btw298.

VCAKE 2.0 – Genetic Sequence Assembler

VCAKE 2.0

:: DESCRIPTION

VCAKE (Verified Consensus Assembly by K-mer Extension) is a genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error. This software is currently geared towards de novo assembly of Illumina’s Solexa Sequencing data.

::DEVELOPER

the Corbin Jones Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OsX / Windows
C Compiler

:: DOWNLOAD

VCAKE

:: MORE INFORMATION

Citation:

William R. Jeck et al.
Extending assembly of short DNA sequences to handle error
Bioinformatics (2007) 23 (21): 2942-2944.