:: DESCRIPTION
HMMTOP is an automatic server for predicting transmembrane helices and topology of proteins
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
G.E Tusnády and I. Simon (2001)
The HMMTOP transmembrane topology prediction server
Bioinformatics 17, 849-850
:: DESCRIPTION
SherLoc2 predicts animal, plant and fungal protein subcellualr localizations using sequence-based and text-based features.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Briesemeister, S, Blum, T, Brady, S, Lam, Y, Kohlbacher, O, and Shatkay, H (2009).
SherLoc2: a high-accuracy hybrid method for predicting subcellular localization of proteins
J. Proteome Res., 8(11):5363–5366
:: DESCRIPTION
seqjoin is used to predict the complete cDNA insert sequence of partially sequenced cDNA clones. The clones’ partial experimental sequence are matched to a database of complete cDNA sequence. If a match is found, the clone’s insert sequence is predicted from the vector sequence, the sequence of the database cDNA sequence entry that was matched and the experimental, partial clone sequence. seqjoin is based on the output of the sequence analysis programs phred, phrap, cross_match and also uses the Emboss package.
::DEVELOPER
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Orphelia is a metagenomic ORF finding tool for the prediction of protein coding genes in short, environmental DNA sequences with unknown phylogenetic origin [1]. Orphelia is based on a two-stage machine learning approach that was recently introduced by our group. After the initial extraction of open reading frames (ORFs), linear discriminants are used to extract features from those ORFs. Subsequently, an artificial neural network combines the features and computes a gene probability for each ORF in a fragment. A greedy strategy computes a likely combination of high scoring ORFs with an overlap constraint.
::DEVELOPER
the Department of Bioinformatics of the University of Göttingen
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
K. J. Hoff, T. Lingner, P. Meinicke, M. Tech (2009)
Orphelia: predicting genes in metagenomic sequencing reads
Nucleic Acids Research, 37:W101-W105.
:: DESCRIPTION
I-sites is a method for predicting initiation sites of folding protein sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citaiton
Bystroff C & Baker D. (1998).
Prediction of local structure in proteins using a library of sequence-structure motifs.
J Mol Biol 281, 565-77.
:: DESCRIPTION
NucPred (pronounced newk-pred) analyses a eukaryotic protein sequence and predicts if the protein: spends at least some time in the nucleus or spends no time in the nucleus. Don’t forget that proteins can have multiple functions and/or multiple subcellular locations. However, if a protein is already known to be secreted or is an integral membrane protein, a second role as a nuclear protein is not likely. NucPred will make a small number of confident but contradictory predictions like this. So please use all sources of biological information (both real and predicted) when interpreting the results.
::DEVELOPER
Stockholm Bioinformatics Center
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
The source code to NucPred is freely available to all under the GNU Public License (GPL)
Citation:
NucPred – Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
