PREDITOR – Predicting Torsion Angles in Proteins from NMR Chemical Shifts and/or Homology

PREDITOR

:: DESCRIPTION

PREDITOR is a program for PREDIcting φ, ψ, χ1, and ω TORsion angles in proteins from 13C, 15N and 1H chemical shifts and sequential homology. PREDITOR 30o-accuracy of predicting φ and ψ is close to 90%. The average χ1 accuracy is 84% while the ω accuracy is 99.98% for trans peptide bond identification and 93% for cis peptide bond identification.

::DEVELOPER

the Wishart Research Group, University of Alberta

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

PREDITOR: a web server for predicting protein torsion angle restraints.
Berjanskii MV, Neal S, Wishart DS.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W63-9.

Neighborhood Correlation 2.1 – Homology Identification

Neighborhood Correlation 2.1

:: DESCRIPTION

Neighborhood Correlation is a novel homology identification method based on the observation that gene duplication and domain insertion result in different topological structures in the sequence similarity network

::DEVELOPER

Durand Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX
C++ Compiler
Python

:: DOWNLOAD

Neighborhood Correlation

:: MORE INFORMATION

Citation

Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins
Song N, Joseph JM, Davis GB, Durand D
PLoS Computational Biology 4(5): e1000063
doi:10.1371/journal.pcbi.1000063

alfy 1.5 – Alignment-Free local homologY

alfy 1.5

:: DESCRIPTION

alfy is a computer program for comparing one or more query DNA sequences to a set of subject sequences. For each query sequence the output consists of a list of intervals indicating the closest homologue among the set of subject sequences.

::DEVELOPER

Bernhard Haubold

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX
C Compiler

:: DOWNLOAD

alfy

:: MORE INFORMATION

Citation

Alignment-free detection of local similarity among viral and bacterial genomes.
Domazet-Lošo M, Haubold B.
Bioinformatics. 2011 Jun 1;27(11):1466-72.

TransposonPSI 20100822 – PSI-Blast to Mine (Retro-)Transposon ORF Homologies

TransposonPSI 20100822

:: DESCRIPTION

TransposonPSI is an analysis tool to identify protein or nucleic acid sequence homology to proteins encoded by diverse families of transposable elements. PSI-Blast is used with a collection of (retro-)transposon ORF homology profiles to identify statistically significant alignments. This method can be used to identify potential transposon ORFs within a protein set, or to identify regions of transposon homology within a larger genome sequence. This is particularly useful to identify degenerate transposon homologies within genome sequences that escape identification and masking by using RepeatMasker and an associated nucleotide library of repetitive elements. TransposonPSI has been routinely used to assist in the discovery of mobile elements across eukaryotes including protozoa, plants, fungi, and animals.

::DEVELOPER

Brian Haas @ Broad Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

TransposonPSI

:: MORE INFORMATION