A combined transmembrane topology and signal peptide prediction method.

A combined transmembrane topology and signal peptide prediction method. (2004)

by L Kall, A Krogh, E L Sonnhammer

Venue:

J. Mol. Biol.

Results 1 - 10 of 226

Pfam protein families database

by Robert D. Finn, John Tate, Jaina Mistry, Penny C. Coggill, Stephen John Sammut, Hans-rudolf Hotz, Goran Ceric, Kristoffer Forslund, Sean R. Eddy, Erik L. L. Sonnhammer, Alex Bateman - Nucleic Acids Research, 2008, 36(Database issue): D281–D288

"... Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318 protein families. Pfam is now based not only on the UniProtKB sequence database, but also on NCBI GenP ..."

Abstract - Cited by 771 (13 self) - Add to MetaCart

Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318 protein families. Pfam is now based not only on the UniProtKB sequence database, but also on NCBI GenPept and on sequences from selected metage-nomics projects. Pfam is available on the web from the consortium members using a new, consistent and improved website design in the UK

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Improved prediction of signal peptides -- SignalP 3.0

by Jannick Dyrløv Bendtsen, Henrik Nielsen, Gunnar von Heijne, Søren Brunak - J. MOL. BIOL. , 2004

"... We describe improvements of the currently most popular method for prediction of classically secreted proteins, SignalP. SignalP consists of two different predictors based on neural network and hidden Markov model algorithms, where both components have been updated. Motivated by the idea that the cle ..."

Abstract - Cited by 654 (7 self) - Add to MetaCart

We describe improvements of the currently most popular method for prediction of classically secreted proteins, SignalP. SignalP consists of two different predictors based on neural network and hidden Markov model algorithms, where both components have been updated. Motivated by the idea that the cleavage site position and the amino acid composition of the signal peptide are correlated, new features have been included as input to the neural network. This addition, combined with a thorough error-correction of a new data set, have improved the performance of the predictor significantly over SignalP version 2. In version 3, correctness of the cleavage site predictions have increased notably for all three organism groups, eukaryotes, Gram-negative and Grampositive bacteria. The accuracy of cleavage site prediction has increased in the range from 6-17 % over the previous version, whereas the signal peptide discrimination improvement is mainly due to the elimination of false positive predictions, as well as the introduction of a new discrimination score for the neural network. The new method has also been benchmarked against other available methods. Predictions can be made at the publicly available web server

An HMM posterior decoder for sequence feature prediction that includes homology information

by Lukas Käll, Anders Krogh, Erik L. Sonnhammer , 2005

"... Motivation: When predicting sequence features like transmembrane topology, signal peptides, coil--coil structures, protein secondary structure or genes, extra support can be gained from homologs. ..."

Abstract - Cited by 45 (3 self) - Add to MetaCart

Motivation: When predicting sequence features like transmembrane topology, signal peptides, coil--coil structures, protein secondary structure or genes, extra support can be gained from homologs.

Analysis Tool Web Services from the EMBL-EBI

by Hamish Mcwilliam, Weizhong Li, Mahmut Uludag, Silvano Squizzato, Young Mi Park, Nicola Buso, Andrew Peter Cowley, Rodrigo Lopez - Nucleic Acids Res , 2013

"... Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in th ..."

Abstract - Cited by 36 (3 self) - Add to MetaCart

Since 2004 the European Bioinformatics Institute (EMBL-EBI) has provided access to a wide range of databases and analysis tools via Web Services interfaces. This comprises services to search across the databases available from the EMBL-EBI and to explore the network of cross-references present in the data (e.g. EB-eye), services to retrieve entry data in various data formats and to access the data in specific fields (e.g. dbfetch), and analysis tool services, for example, sequence similarity search (e.g. FASTA and NCBI BLAST), multiple sequence alignment (e.g. Clustal Omega and MUSCLE), pairwise sequence alignment and protein functional analysis (e.g. InterProScan and Phobius). The REST/SOAP Web Services

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Recent advances in developing web-servers for predicting protein attributes

by Kuo-chen Chou, Hong-bin Shen , 2009

"... ..."

Abstract - Cited by 28 (4 self) - Add to MetaCart

Abstract not found

Prediction of subcellular localization using sequence-biased recurrent networks

by Mikael Bodén, John Hawkins - Bioinformatics , 2005

"... doi:10.1093/bioinformatics/bti372 ..."

Abstract - Cited by 26 (0 self) - Add to MetaCart

doi:10.1093/bioinformatics/bti372

2007a) Identification of diverse archaeal proteins with class III signal peptides cleaved by distinct archaeal prepilin peptidases

by Adriana Oliveira Stahl, Sonja-v. Albers, Jessica C. Kissinger, Arnold J. M. Driessen - J Bacteriol

"... Most secreted archaeal proteins are targeted to the membrane via a tripartite signal composed of a charged N terminus and a hydrophobic domain, followed by a signal peptidase-processing site. Signal peptides of archaeal flagellins, similar to class III signal peptides of bacterial type IV pilins, ar ..."

Abstract - Cited by 25 (6 self) - Add to MetaCart

Most secreted archaeal proteins are targeted to the membrane via a tripartite signal composed of a charged N terminus and a hydrophobic domain, followed by a signal peptidase-processing site. Signal peptides of archaeal flagellins, similar to class III signal peptides of bacterial type IV pilins, are distinct in that their processing sites precede the hydrophobic domain, which is crucial for assembly of these extracytoplasmic structures. To identify the complement of archaeal proteins with class III signal sequences, a PERL program (FlaFind) was written. A diverse set of proteins was identified, and many of these FlaFind positives were encoded by genes that were cotranscribed with homologs of pilus assembly genes. Moreover, structural conservation of primary sequences between many FlaFind positives and subunits of bacterial pilus-like structures, which have been shown to be critical for pilin assembly, have been observed. A subset of pilin-like FlaFind positives contained a conserved domain of unknown function (DUF361) within the signal peptide. Many of the genes encoding these proteins were in operons that contained a gene encoding a novel euryarchaeal prepilin-peptidase, EppA, homolog. Heterologous analysis revealed that Methanococcus maripaludis DUF361-containing proteins were specifically processed by the EppA homolog of this archaeon. Conversely, M. mari-paludis preflagellins were cleaved only by the archaeal preflagellin peptidase FlaK. Together, the results reveal

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