Sircah 1.0 – Detection and Visualization of Alternative Transcripts

Sircah 1.0

:: DESCRIPTION

Sircah is an application written in python that dectects and visualises alternative splicing events using spliced alignments.Sircah takes as input transcript models in the GFF3 format allowing the user the flexibility to choose the sources of evidence for the use in detecting alternative transcription. Such transcript models may come from the gene prediction pipelines of genome databases or from spliced alignments of ESTs or proteins against the genome.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Sircah

:: MORE INFORMATION

Citation

Sircah: a tool for the detection and visualization of alternative transcripts.
Harrington ED, Bork P.
Bioinformatics. 2008 Sep 1;24(17):1959-60. Epub 2008 Jul 17.

 

OmegaPlus 2.2.2 – Detection of Selective Wweeps in Whole-genome Datasets

OmegaPlus 2.2.2

:: DESCRIPTION

OmegaPlus is a parallel tool for rapid & scalable detection of selective sweeps in whole-genome datasets

::DEVELOPER

the Exelixis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 OmegaPlus

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 1;28(17):2274-5. doi: 10.1093/bioinformatics/bts419.
OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole-genome datasets.
Alachiotis N, Stamatakis A, Pavlidis P.

Framedp 1.22 – Sensitive Peptide Detection on Noisy Matured Sequences

Framedp 1.22

:: DESCRIPTION

FrameDP is a self-training integrative pipeline for predicting CDS in transcripts which can adapt itself to different levels of sequence qualities.

:: DEVELOPER

Framedp Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Framedp

:: MORE INFORMATION

Citation:

Jérôme Gouzy, Sébastien Carrere1 and Thomas Schiex
FrameDP: sensitive peptide detection on noisy matured sequences
Bioinformatics (2009) 25 (5): 670-671.

HHblits 3.2.0 – Homology Detection by Iterative HMM-HMM Comparison

HHblits 3.2.0

:: DESCRIPTION

HHblits is the first iterative method based on the pairwise comparison of profile Hidden Markov Models. In benchmarks it achieves better runtimes than other iterative sequence search methods such as PSI-BLAST or HMMER3 by using a fast prefilter based on profile-profile comparison. Furthermore, HHblits greatly improves upon PSI-BLAST and HMMER3 in terms of sensitivity/selectivity and alignment quality.

::DEVELOPER

Söding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

  Part of HH-suite

:: MORE INFORMATION

Citation

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment.
Remmert M, Biegert A, Hauser A, Söding J.
Nat Methods. 2011 Dec 25;9(2):173-5. doi: 10.1038/nmeth.1818.

FUGUE 20160606 – Protein Structure Prediction using Remote Homology Detection

FUGUE 20160606

:: DESCRIPTION

FUGUE is a program for recognizing distant homologues by sequence-structure comparison. It utilizes environment-specific substitution tables and structure-dependent gap penalties, where scores for amino acid matching and insertions/deletions are evaluated depending on the local environment of each amino acid residue in a known structure. Given a query sequence (or a sequence alignment), FUGUE scans a database of structural profiles, calculates the sequence-structure compatibility scores and produces a list of potential homologues and alignments.

::DEVELOPER

the Mizuguchi Laboratory.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 FUGUE

:: MORE INFORMATION

Citation

J. Shi, T. L. Blundell, and K. Mizuguchi (2001).
FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure- dependent gap penalties.
J. Mol. Biol., 310, 243-257.

GESS 1.0 – Exon-skipping Scanner Detection program for RNA-seq data

GESS 1.0

:: DESCRIPTION

GESS (graph-based exon-skipping scanner) is a novel computational method for de novo detection of skipping event sites from raw RNA-seq reads without prior knowledge of gene annotations, as well as for determining the dominant isoform generated from such sites.

::DEVELOPER

Jin Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 GESS

:: MORE INFORMATION

Citation

Ye Z, Chen Z, Lan X, Hara S, Sunkel B, Huang TH, Elnitski L, Wang Q, Jin VX.
Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors.
Nucleic Acids Res. 2014 Mar 1;42(5):2856-69.

SubSeqer – Detection and Identification of Repetitive Elements in low-complexity Sequences

SubSeqer

:: DESCRIPTION

SubSeqer is a web-tool which uses graphical visualization methods borrowed from protein interaction studies to identify and characterize repetitive elements in low-complexity sequences.

::DEVELOPER

Parkinson lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Apr 1;24(7):1016-7. doi: 10.1093/bioinformatics/btn073. Epub 2008 Feb 26.
SubSeqer: a graph-based approach for the detection and identification of repetitive elements in low-complexity sequences.
He D, Parkinson J.

Magnolya 0.15 – Detection of Copy Number Variation

Magnolya 0.15

:: DESCRIPTION

Magnolya is an algorithm for de novo detection of copy number variation. Magnolya directly compares two next-generation sequencing datasets.

::DEVELOPER

The Delft Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

 Magnolya

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Oct 9. [Epub ahead of print]
De novo detection of copy number variation by co-assembly.
Nijkamp JF, van den Broek MA, Geertman JM, Reinders MJ, Daran JM, de Ridder D.

SoftSearch 1.0 – Structural Variant (SV) Detection tool

SoftSearch 1.0

:: DESCRIPTION

SoftSearch is a sensitive structural variant detection (SV) detection tool for Illumina paired-end next-generation sequencing data. SoftSearch simultaneously utilizes soft-clipping and read-pair strategies for detecting SVs to increase sensitivity.

::DEVELOPER

Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 SoftSearch

:: MORE INFORMATION

Citation

PLoS One. 2013 Dec 16;8(12):e83356. doi: 10.1371/journal.pone.0083356. eCollection 2013.
SoftSearch: integration of multiple sequence features to identify breakpoints of structural variations.
Hart SN1, Sarangi V1, Moore R1, Baheti S1, Bhavsar JD1, Couch FJ2, Kocher JP

COMA 1.10 – Detection of Distant Evolutionary Relationships

COMA 1.10

:: DESCRIPTION

COMA (Comparison Of Multiple Alignments) is a method for detection of distant evolutionary relationship (homology) through comparison of multiple protein sequence alignments. For convenience, the COMA software package includes programs for constructing profiles from multiple alignments, generating a profile database from a set of profiles, searching a profile (multiple alignment) against a profile database, etc. COMA output consists of pairwise alignments between profiles (multiple alignments) with estimated values of statistical significance, which indicates the probability that the aligned pair of profiles is a random match.

::DEVELOPER

VU Institute of Biotechnology

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 COMA

:: MORE INFORMATION

Citation

Margelevičius M., Venclovas Č. (2010)
Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparisons.
BMC Bioinformatics, 2010 11:89.