GMV 0.1 – Genome Majority Vote Gene Start Correction Software

GMV 0.1

:: DESCRIPTION

The GMV pipeline works as follows. Input is a set of genomes. The pipeline runs PRODIGAL gene predictions on all genomes, runs pan-reciprocal BLAST, and identifies ortholog sets. For a given set of orthologous genes, if the positions of the PRODIGAL selected starts coincide in a multiple sequence alignment, they are accepted. If they do not coincide, a consistent start position is sought where a majority of the highest-scoring PRODIGAL selected sites coincide. If such a position is found, it is accepted, and the predictions are changed for the outlying genes. Otherwise, no start site prediction is made for the ortholog set.

::DEVELOPER

Michael Wall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

GMV

:: MORE INFORMATION

Citation

Genome majority vote improves gene predictions.
Wall ME, Raghavan S, Cohn JD, Dunbar J.
PLoS Comput Biol. 2011 Nov;7(11):e1002284.

DistPCoA – Principal Coordinate Analysis with Correction for Negative Eigenvalues

DistPCoA

:: DESCRIPTION

DistPCoA performs Principal Coordinate Analysis (PCoA; Gower 1966) with the option of correcting for negative eigenvalues.

::DEVELOPER

Pierre Legendre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

MacOsX / Windows

:: DOWNLOAD

DistPCoA

:: MORE INFORMATION

CMC 20100422 – Cross-mapping Correction software

CMC 20100422

:: DESCRIPTION

CMC (Cross-mapping Correction)is a software of modern high-throughput technologies which enable deep sequencing of non-coding RNA species, such as miRNAs, on an unprecedented scale. When mapping such small RNAs to the genome, cross-mapping may occur, in which RNA sequences originating from one genomic locus are inadvertently mapped to a different locus. This may give rise to spurious novel RNAs, as well as spurious editing sites in known miRNAs. The cross-mapping correction software is a Python script that aims to correct for such cross-mapping effects.

::DEVELOPER

FANTOM

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOSX / Windows
Python
NumPy

:: DOWNLOAD

CMC

:: MORE INFORMATION

Citation

De Hoon, M.J.L., et al. (2010):
Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries.
Genome Research 20: 257-264 (2010).

ICORN 0.97 – Iterative Correction of Reference Nucleotide

ICORN 0.97

:: DESCRIPTION

iCORN is a software to correct reference genome sequences. The main idea is to iteratively map reads and find differences in the sequence: as the sequence is corrected a greater proportion of the reads are able to map. Results are exported for Artemis or Gap4 for visualisation.

::DEVELOPER

Thomas D. Otto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

ICORN

:: MORE INFORMATION

Citation

Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology.
Otto TD, Sanders M, Berriman M and Newbold C
Bioinformatics (Oxford, England) 2010;26;14;1704-7

RNABC 1.11 – RNA Backbone Correction

RNABC 1.11

:: DESCRIPTION

RNABC (RNA Backbone Correction) is designed for reducing the steric clashes in dinucleotides of existing RNA backbone structures. It first fixes the phosphate and base positions, which are the clearest parts in X-ray crystallography structure, and then reconstructs the remaining atoms of the dinucleotide using forward kinematics and conjugate gradient method. The input parameters, like bond lengths, bond angles, and sugar pucker types, are from canonical values or specified by users. The output results cluster the possible suite conformations (from base to base) without steric clashes.

::DEVELOPER

Xueyi Wang & Prof. Jack Snoeyink
Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

Windows / Mac / Linux

:: DOWNLOAD

RNABC

:: MORE INFORMATION

RNABC is described in X. Wang, G. Kapral, L. Murray, D. Richardson, J. Richardson & J. Snoeyink. “RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone”. Journal Mathematical Biology (published January 2008, doi: 10.1007/s00285-007-0082)

RNABC is free software available under the terms of its own BSD-style license.