Tag: Short Sequence Reads

IsoInfer 0.9.1 – Inference of Isoforms from Short Sequence Reads

IsoInfer 0.9.1

:: DESCRIPTION

IsoInfer is a program to infer isoforms based on short RNA-Seq (single-end and paired-end) reads, exon-intron boundary and TSS/PAS information.

::DEVELOPER

Wei Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C/C++ Compiler

:: DOWNLOAD

 IsoInfer

:: MORE INFORMATION

Citation

J Comput Biol. 2011 Mar;18(3):305-21. doi: 10.1089/cmb.2010.0243.
Inference of isoforms from short sequence reads.
Feng J1, Li W, Jiang T.

QPALMA 0.9.3 – Optimal Spliced Alignments of Short Sequence Reads

QPALMA 0.9.3

:: DESCRIPTION

QPALMA is a software for computing accurate spliced alignments which takes advantage of the read’s quality information as well as computational splice site predictions. Our method uses a training set of spliced reads with quality information and known alignments. It uses a large margin approach similar to support vector machines to estimate its parameters to maximize alignment accuracy.

::DEVELOPER

the Biomedical Informatics Lab of Prof. Dr. Gunnar Rätsch

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • Python

:: DOWNLOAD

 QPALMA

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Aug 15;24(16):i174-80.
Optimal spliced alignments of short sequence reads.
De Bona F, Ossowski S, Schneeberger K, Rätsch G.