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a database for Mycobacterium secretome analysis
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MycoSec

SignalP

It predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks and hidden Markov models.

SecretomeP

The SecretomeP 2.0 server produces ab initio predictions of non-classical i.e. not signal peptide triggered protein secretion. The method queries a large number of other feature prediction servers to obtain information on various post-translational and localizational aspects of the protein, which are integrated into the final secretion prediction.

TMHMM

TransMembrane prediction using Hidden Markov Models -- is a program for predicting transmembrane helices based on a hidden Markov model. It reads a FASTA formatted protein sequence and predicts locations of transmembrane, intracellular and extracellular regions.

TATFIND

It predicts the presence of prokaryotic Twin-Arginine Translocation (Tat) signal peptides.

Pred-Lipo

The method is also very sensitive and specific in the detection of secretory signal peptides and in terms of overall accuracy outperforms even SignalP, which is the top-scoring method for the prediction of signal peptides.

IMG

The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis and annotation of all publicly available genomes from three domains of life in a uniquely integrated context.

NCBI

The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health.

WebLogo 3

It is a web based application designed to make the generation of sequence logos as easy and possible. Sequence logos are a graphical representation of an amino acid or nucleic acid multiple sequence alignment developed by Tom Schneider and Mike Stephens.

CAI Calculator 2

CAI is a single value measurement that summarizes the codon usage of a gene relative to the codon usage of a reference set of genes. A higher CAI value usually suggests that the gene of interest is likely to be highly expressed.

codonw 1.4.4

The CodonW application was designed to be a package for codon usage analysis. It was designed to simplify Multivariate Analysis (MVA) of codon usage.Additional analyses of codon usage include investigation of optimal codons, codon and dinucleotide bias, and/or base composition.

 

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