GeneSeqer 20140226 – Gene Identification Tool

GeneSeqer 20140226

:: DESCRIPTION

GeneSeqer is a gene identification tool based on spliced alignment or “spliced threading” of ESTs with a genomic query sequence. In a spliced alignment, aligned residues in the genomic sequence are assigned exon status. Introns are identfied as large gaps in the alignment, typically (but not necessarily) flanked by the consensus GT and AG dinucleotides at the donor and acceptor sites, respectively. The optimal alignment is derived by scoring for both sequence similarity and potential splice site strength. The program is designed to handle alignment of a large number of ESTs on a long genomic query sequence (BAC size). Therefore, the ESTs are pre-screened, and only ESTs with sufficient significant matching are fully aligned.

::DEVELOPER

The Brendel Group @ Indiana University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

GeneSeqer

:: MORE INFORMATION

Citation

Brendel, V., Xing, L. and Zhu, W.
Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus.
Bioinformatics 20(7), 1157-1169 (2004).

NPACT 2.3.1 – N-Profile Analysis Computational Tool

NPACT 2.3.1

:: DESCRIPTION

NPACT is a computational and graphical representation tool for gene identification and sequence annotation. NPACT identifies sequence segments of any length with statistically-significant 3-base compositional periodicities and associated with ORF structures .

::DEVELOPER

NPACT team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX

:: DOWNLOAD

NPACT

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Jun 4. pii: btv339.
Quantitative frame analysis and the annotation of GC-rich (and other) prokaryotic genomes. An application to Anaeromyxobacter dehalogenans.
Oden S, Brocchieri L

GIPS 1.7 – Gene Identification via Phenotype Sequencing

GIPS 1.7

:: DESCRIPTION

GIPS software considers a range of experimental and analysis choices in sequencing-based forward genetics studies within an integrated probabilistic framework, which enables direct gene cloning from the sequencing of several unrelated mutants of the same phenotype without the need to create segregation populations.

::DEVELOPER

GIPS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / WIndows/ MacOsX
Java

:: DOWNLOAD

GIPS

:: MORE INFORMATION

Citation

GIPS: A Software Guide to Sequencing-based Direct Gene Cloning in Forward Genetics Studies.
Hu H, Wang W, Zhu Z, Zhu J, Tan D, Zhou Z, Mao C, Chen X.
Plant Physiol. 2016 Feb 3. pii: pp.01327.2015.

Int-Path – Causal Gene Identification and Gene Regulatory Pathway Inference

Int-Path

:: DESCRIPTION

Int-Path is to implement an algorithm to infer the causal gene for the expression variation and the underlying regulatory pathway.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
java

:: DOWNLOAD

Int-Path

:: MORE INFORMATION

Citation

Zhidong Tu, Li Wang, Michelle N. Arbeitman, Ting Chen and Fengzhu Sun
An integrative approach for causal gene identification and gene regulatory pathway inference
Bioinformatics (2006) 22 (14): e489-e496.