Tag: Locate

pediSNP – Locate Meiotic Recombination Sites from SNPs

pediSNP

:: DESCRIPTION

pediSNP is designed to provide an analysis of Single Nucleotide Polymorphism (SNP) data from a pedigree of two generations: two parents with two or more children. It has been designed based on genotype data exported from Affymetrix CNAT 4.0, Illumina Beadstudio, as well as data downloaded from the HapMap project. However, any SNP data is formatted as any one of these three sources, pediSNP can analyze it.

::DEVELOPER

the Pevsner Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Locations and patterns of meiotic recombination in two-generation pedigrees.
Ting JC, Roberson ED, Currier DG, Pevsner J.
BMC Med Genet. 2009 Sep 17;10:93. doi: 10.1186/1471-2350-10-93.

PatScan – Locate Patterns in DNA or Protein FASTA files

PatScan

:: DESCRIPTION

PatScan (scan_for_matches) is a pattern matcher which searches protein or nucleotide (DNA, RNA, tRNA etc.) sequence archives for instances of a pattern which you input.

::DEVELOPER

Ross Overbeek (overbeek@mcs.anl.gov); David Joerg and Morgan Price

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 PatScan

:: MORE INFORMATION

Breakpointer 0.1 – Locate Vreakpoints of SVs from Single-end Reads

Breakpointer 0.1

:: DESCRIPTION

Breakpointer is a fast algorithm to locate breakpoints of structural variants (SVs) from single-end reads produced by next-generation sequencing (NGS). By taking advantage of local non-uniform read distribution and misalignments created by SVs, Breakpointer scans the alignment of single-end reads to identify regions containing potential breakpoints. The detection of such break-points can indicate insertions longer than the read length and SVs located in repetitve regions which might be missd by other methods. Thus, Breakpointer complements existing methods to locate SVs from single-end reads.

::DEVELOPER

Sun, Ruping

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Perl 

:: DOWNLOAD

  Breakpointer

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Apr 1;28(7):1024-5. Epub 2012 Feb 1.
Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads.
Sun R, Love MI, Zemojtel T, Emde AK, Chung HR, Vingron M, Haas SA.