Tag: Transcript Sequence

PIntron 1.4.2 – Gene-structure Prediction based on Spliced Alignments of Transcript Sequences.

PIntron 1.4.2

:: DESCRIPTION

PIntron is a novel pipeline for gene-structure prediction based on spliced alignment of transcript sequences (ESTs and mRNAs) against a genomic sequence.

::DEVELOPER

AlgoLab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Python
  • Perl
  • gcc, make

:: DOWNLOAD

 PIntron

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 Apr 12;13 Suppl 5:S2. doi: 10.1186/1471-2105-13-S5-S2.
PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text.
Pirola Y, Rizzi R, Picardi E, Pesole G, Della Vedova G, Bonizzoni P.

Methods Mol Biol. 2015;1269:173-88. doi: 10.1007/978-1-4939-2291-8_11.
Transcriptome assembly and alternative splicing analysis.
Bonizzoni P1, Della Vedova G, Pesole G, Picardi E, Pirola Y, Rizzi R.

IsoCon 0.3.2 – Deriving Finished Transcript Sequences from Iso-Seq reads

IsoCon 0.3.2

:: DESCRIPTION

IsoCon is a tool for reconstructing highly similar sequences present in a dataset of from long noisy reads

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

IsoCon

:: MORE INFORMATION

Citation

Kristoffer Sahlin, Marta Tomaszkiewicz, Kateryna D. Makova, Paul Medvedev
Deciphering highly similar multigene family transcripts from iso-seq data with isocon.
Nature Communications, 9(1):4601, 2018

ExonScan 1.0 – Simulating the RNA Splicing Pattern of a Primary Transcript Sequence

ExonScan 1.0

:: DESCRIPTION

ExonScan expects a primary transcript sequence, preferably excluding the first and last exon. It also currently needs at least about 20 bases upstream of the first exon it can locate, and at least about 60 bases downstream of the last. Numbers in the sequence are discarded, so you can cut and paste from, e.g., a GenBank file.

::DEVELOPER

Christopher Burge Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Cell. 2004 Dec 17;119(6):831-45.
Systematic identification and analysis of exonic splicing silencers.
Wang Z, Rolish ME, Yeo G, Tung V, Mawson M, Burge CB.