EcoliWiki - User contributions [en]

HHomp

2009-09-14T14:36:11Z

MichaelR: Table edited by MichaelR via TableEdit

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{{See|Help:Bioinformatics Tools|tools}}

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!align=left {{table heading style}} |Link/URL:
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[http://toolkit.tuebingen.mpg.de/hhomp HHomp]
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!align=left {{table heading style}} |What:
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Outer membrane protein prediction and classification
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!align=left {{table heading style}} |Who:
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Michael Remmert -
Dep. of Protein Evolution at the Max-Planck Institute for Developmental Biology

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== Short Description ==
[[Image:HHomp_home.jpg|300px|thumb|right|Home Page]]

HHomp is a tool available for the prediction and classification of outer membrane proteins<ref name='PMID:19429691'/>.

Outer membrane proteins (OMPs) are the transmembrane proteins found in the outer membranes of Gram-negative bacteria, mitochondria and plastids. HHomp identifies proteins as OMPs by detecting their homologous relationships to known OMPs using sequence similarity. Given an input sequence, HHomp builds a profile hidden Markov model (HMM) and compares it with an OMP database by pairwise HMM comparison, integrating OMP predictions by PROFtmb. A crucial ingredient is the OMP database, which contains profile HMMs for over 20 000 putative OMP sequences.

The HHomp webserver consists of an OMP prediction and searching interface and a browsing interface for the underlying OMP database. With the prediction interface, the user can search the database with a query protein sequence. Various parameters for alignment building and searching can be modified (explained in the online help). After a few minutes, the server returns a graphical overview of the matched regions, a detailed and annotated list of matched OMP database HMMs and the corresponding alignments. An alternative view of the alignments can be selected, in which the columns of the aligned profile HMMs are represented as coloured histograms. The detected OMP HMMs are linked to the browsing interface with detailed description pages for the OMP clusters, containing alignments and 3D models for the TM domain if available.

== Links ==
http://toolkit.tuebingen.mpg.de/hhomp

http://toolkit.lmb.uni-muenchen.de/hhomp

== Requirements ==
Webserver

== User notes ==

== See Also ==
Download HHomp & OMP database: ftp://ftp.tuebingen.mpg.de/pub/protevo/HHomp

== References ==
{{RefHelp}}
<references/>
[[Category:Bioinformatics Tools]]
[[Category:E._coli_protein_localization]]

HHomp

2009-09-14T14:34:05Z

MichaelR: Update HHomp-information

{{Pagetop}}<br />
{{See|Help:Bioinformatics Tools|tools}}

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!align=left {{table heading style}} |Link/URL:
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[http://toolkit.tuebingen.mpg.de/hhomp# HHomp]
|-
!align=left {{table heading style}} |What:
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Outer membrane protein prediction
|-
!align=left {{table heading style}} |Who:
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Dep. of Protein Evolution at the Max-Planck Institute for Developmental Biology

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== Short Description ==
[[Image:HHomp_home.jpg|300px|thumb|right|Home Page]]

HHomp is a tool available for the prediction and classification of outer membrane proteins<ref name='PMID:19429691'/>.

Outer membrane proteins (OMPs) are the transmembrane proteins found in the outer membranes of Gram-negative bacteria, mitochondria and plastids. HHomp identifies proteins as OMPs by detecting their homologous relationships to known OMPs using sequence similarity. Given an input sequence, HHomp builds a profile hidden Markov model (HMM) and compares it with an OMP database by pairwise HMM comparison, integrating OMP predictions by PROFtmb. A crucial ingredient is the OMP database, which contains profile HMMs for over 20 000 putative OMP sequences.

The HHomp webserver consists of an OMP prediction and searching interface and a browsing interface for the underlying OMP database. With the prediction interface, the user can search the database with a query protein sequence. Various parameters for alignment building and searching can be modified (explained in the online help). After a few minutes, the server returns a graphical overview of the matched regions, a detailed and annotated list of matched OMP database HMMs and the corresponding alignments. An alternative view of the alignments can be selected, in which the columns of the aligned profile HMMs are represented as coloured histograms. The detected OMP HMMs are linked to the browsing interface with detailed description pages for the OMP clusters, containing alignments and 3D models for the TM domain if available.

== Links ==
http://toolkit.tuebingen.mpg.de/hhomp

http://toolkit.lmb.uni-muenchen.de/hhomp

== Requirements ==
Webserver

== User notes ==

== See Also ==
Download HHomp & OMP database: ftp://ftp.tuebingen.mpg.de/pub/protevo/HHomp

== References ==
{{RefHelp}}
<references/>
[[Category:Bioinformatics Tools]]
[[Category:E._coli_protein_localization]]

HHpred

2009-09-14T14:20:10Z

MichaelR: Update HHpred-information

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[http://toolkit.tuebingen.mpg.de/hhpred HHpred]
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!align=left {{table heading style}} |What:
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Detect remote homologies by comparison of hidden Markov models
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!align=left {{table heading style}} |Who:
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Dep. of Protein Evolution at the Max-Planck Institute for Developmental Biology

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== Short Description ==
{{UserContentHelp}}
[[Image:HHpred_home.jpg|right|thumb|300px|Home Page]]
HHsearch is a program for protein sequence searching that is free for non-commercial use.<ref name='PMID:15531603'/> HHpred is a free protein function and protein structure prediction server based on the HHsearch method.<ref name='PMID:15980461'/> HHpred/HHsearch are among the most popular methods for protein structure prediction and the detection of remotely related sequences, having been cited over 380 times.

Sequence searches are frequently performed by biologists to infer the function of an unknown protein from its sequence. For this purpose, the protein's sequence is compared to the sequences of other proteins in public databases and its function is deduced from those of the most similar sequences. Often, no sequences with annotated functions can be found in such a search. In this case, more sensitive methods are required to identify more remotely related proteins or protein families. From these relationships, hypotheses about the protein's functions, structure, and domain composition can be inferred. HHsearch performs searches with a protein sequence through databases. The HHpred server and the HHsearch software package offer many popular, regularly updated databases, such as the Protein Data Bank, as well as the InterPro, Pfam, COG, and SCOP databases.

HHpred/HHsearch belongs to the class of profile-profile comparison tools, which includes the most sensitive sequence search methods to date.<ref name='PMID:10975570'/><ref name='PMID:14500884'/><ref name='PMID:16713709'/><ref name='PMID:15531603'/> They represent both the query sequence and the database sequences by sequence profiles, also called position-specific scoring matrices (PSSMs). Profiles are calculated from a multiple sequence alignment of related sequences which are typically collected using the PSI-BLAST program from the National Center for Biotechnology Information (NCBI). A profile is a matrix containing for each position in the query sequence the similarity score for the 20 amino acids. These scores are calculated from the frequencies of the amino acids at the corresponding positions in the multiple sequence alignment. Because profiles contain much more information than a single sequence (e.g. the position-specific degree of conservation), profile-profile comparison methods are much more powerful than sequence-sequence comparison methods like BLAST or profile-sequence comparison methods like PSI-BLAST.<ref name='PMID:10975570'/>

HHpred/HHsearch represents query and database proteins by profile hidden Markov models (HMMs), an extension of sequence profiles which also record position-specific amino acid insertion and deletion frequencies. HHsearch searches a database of HMMs with a query HMM. Before starting the search through the actual database of HMMs, HHsearch/HHpred builds a multiple sequence alignment of related sequences using a context-specific version of PSI-BLAST, called CSI-BLAST. From this alignment, a profile HMM is calculated. The databases contain HMMs that are precalculated in the same fashion using PSI-BLAST. The output of HHpred and HHsearch is a ranked list of database matches (including E-values and probabilities for a true relationship) and the pairwise query-database sequence alignments. A search through the PDB database of proteins with solved 3D structure takes a few minutes. If a significant match with a protein of known structure (a "template") is found in the PDB database, HHpred allows to build a homology model using MODELLER software, starting from the pairwise query-template alignment.

Applications of HHpred/HHsearch include protein structure prediction, function prediction, domain prediction, domain boundary prediction, and evolutionary classification of proteins. In the CASP7 benchmark experiment, HHpred5 was ranked 2nd out of 68 automatic structure prediction servers, while being more than 50 times faster than the best 20 servers.<ref name='PMID:17894354'/>

== Links ==
http://toolkit.tuebingen.mpg.de/hhpred

http://toolkit.lmb.uni-muenchen.de/hhpred
== Requirements ==
Webserver

== User notes ==

== See Also ==
CASP website: http://predictioncenter.org/

Homology detection of outer membrane proteins: [http://ecoliwiki.net/colipedia/index.php/HHomp HHomp]
== References ==
{{RefHelp}}
<references/>
[[Category:Bioinformatics Tools]]