MS-GF+ 20140630 – Database search for Peptide Identification

MS-GF+ 20140630

:: DESCRIPTION

MS-GF+ is a new MS/MS database search tool that is sensitive (it identifies more peptides than other database search tools and as many peptides as spectral library search tools) and universal (works well for diverse types of spectra, different configurations of MS instruments and different experimental protocols).

::DEVELOPER

CCMS The Center for Computational Mass Spectrometry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows/ MacOsX
Java

:: DOWNLOAD

MS-GF+

:: MORE INFORMATION

Citation

MS-GF+ makes progress towards a universal database search tool for proteomics.
Kim S, Pevzner PA.
Nat Commun. 2014 Oct 31;5:5277. doi: 10.1038/ncomms6277.

FREAD 3.0.1 – Database Search Loop Structure Prediction protocol

FREAD 3.0.1

:: DESCRIPTION

FREAD is a database search loop structure prediction protocol. Loops are generally located in the protein’s surface and they are known to be notoriously difficult to predict.The basic assumption of FREAD is that local sequence similarity may determine the backbone structure of a local protein structure if it is constrained within anchor structures.

::DEVELOPER

Oxford Protein Informatics Group (OPIG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux

:: DOWNLOAD

FREAD

Citation

FREAD revisited: Accurate loop structure prediction using a database search algorithm.
Choi Y, Deane CM.
Proteins. 2010 May 1;78(6):1431-40. doi: 10.1002/prot.22658.

Exalign 1.0 – Gene Structural Alignments and Database Search

Exalign 1.0

:: DESCRIPTION

Exalign is a tool that performs alignments of gene exonic structures. In particular it works by aligning arrays representing the exon lengths of genes. While the aligning algorithms used by Exalign are the well known Smith-Waterman and Needleman-Wunsch ones (with a suitable scoring function), the program performs a post-processing step that tries to identify intron gain/loss events (see sections about exon merging).

::DEVELOPER

Bioinformatics Evolution @nd COmparative geNomics lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
C++ Complier

:: DOWNLOAD

Exalign

:: MORE INFORMATION

Citation:

Pavesi G, Zambelli F, Caggese C, Pesole G.
Exalign: a new method for comparative analysis of exon-intron gene structures.
Nucleic Acids Res. 2008 May;36(8):e47. Epub 2008 Apr 8.

COPS Benchmark 2009/6 – Interactive Analysis of Database Search Methods

COPS Benchmark 2009/6

:: DESCRIPTION

The COPS benchmark provides a standardized tool for the analysis of sequence alignment methods, homology search tools and fold recognition techniques which is easy to use. Most importantly, any method can be immediately related to several popular methods. Hence, the server is a useful tool for a wide range of problems encountered in bioinformatics, and in particular for algorithm developers and for all users who need to understand the range of applicability of various alignment methods.

::DEVELOPER

C.A.M.E. – the Center of Applied Molecular Engineering.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX

:: DOWNLOAD

COPS Benchmark

:: MORE INFORMATION

Citation

Frank, K., Gruber, M. & Sippl, M.J.
COPS Benchmark: interactive analysis of database search methods.
Bioinformatics Vol. 26(4), pp. 574-575