AnABlast – Detect potential Coding Regions in DNA by Sequence Comparison

AnABlast

:: DESCRIPTION

AnABlast is an algorithm to discover signals of protein-coding sequences within genomic regions. You can analyze a short nucleotide sequence (up to 25Kb in length or up to 1Mb if you upload the Blast report). It highlights genomic regions with stacked non-significant alignments (protomotifs) which would represent present or ancient protein-coding sequences. It allows to discover new genes in bacteria or exons in eukaryotic organisms.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Methods Mol Biol. 2019;1962:207-214. doi: 10.1007/978-1-4939-9173-0_12.
AnABlast: Re-searching for Protein-Coding Sequences in Genomic Regions.
Rubio A, Casimiro-Soriguer CS, Mier P, Andrade-Navarro MA, Garzón A, Jimenez J, Pérez-Pulido AJ

FrameD 20070223 – Predict Coding Regions in Prokaryotic and Eukaryotic Sequence

FrameD 20070223

:: DESCRIPTION

FrameD is a program that predicts coding regions in prokaryotic and eukaryotic sequences that may contain frameshifts.

::DEVELOPER

Thomas Schiex

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows

:: DOWNLOAD

FrameD

:: MORE INFORMATION

Citation

FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences
Thomas Schiex, Jérôme Gouzy, Annick Moisan, and Yannick de Oliveira
Nucl. Acids. Res. 2003 31: 3738-3741.

ESTScan 3.03 – Detect Coding Regions in DNA/RNA Sequences

ESTScan 3.03

:: DESCRIPTION

ESTScan is a program that can detect coding regions in DNA/RNA sequences, even if they are of low quality (e.g. EST sequences). ESTScan will also detect and correct sequencing errors that lead to frameshifts. ESTScan is not a gene prediction program , nor is it an open reading frame detector. In fact, its strength lies in the fact that it does not require an open reading frame to detect a coding region. As a result, the program may miss a few translated amino acids at either the N or the C terminus, but will detect coding regions with high selectivity and sensitivity.

ESTScan Online Version

::DEVELOPER

The SIB Swiss Institute of Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac OS X

:: DOWNLOAD

ESTScan

:: MORE INFORMATION

Citation

Lottaz C, Iseli C, Jongeneel CV, Bucher P. (2003)
Modeling sequencing errors by combining Hidden Markov models
Bioinformatics 19, ii103-ii112.

Iseli C, Jongeneel CV, Bucher P. (1999)
ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences.
Proc Int Conf Intell Syst Mol Biol.138-48.