Query HOVERGEN using web applications

Acces to several ACNUC databases: EMBL,GenBank,SwissProt, HOVERGEN, HOVERGEN, HOMOLENS, etc.

• WWW-Query Allows to retrieve sequences or families by combining several criteria
• Search families by cross taxa Allows to retrieve families according to complexe taxonomic criteria

Query HOVERGEN proteins

You may enter any word ( sequence name, keyword, species, ...)

Search for protein sequences	Search for protein families
exact match enter a word	exact match enter a word

Check the box if you want to report exact matches only.

Query HOVERGEN nucleotide sequences

You may enter any word ( sequence name, keyword, species, ...)

Search for CDS sequences	Search for CDS families
exact match enter a word	exact match enter a word

Check the box if you want to report exact matches only.

Query HOVERGEN using BLAST

You may blast your sequence against several databases at PBIL.

• Protein BLAST Allows to retrieve protein sequences in HOVERGEN

Query HOVERGEN using HoSeqI

You may search the HOVERGEN family which is the closest of your sequence. Associated alignment and phylogenetic tree are automatically generated.

• HoseqI Allows to retrieve protein family in HOVERGEN

Orthologs search

You can retrieve orthologous and paralogous genes with the FamFetch application. This is a powerful tool allowing you to request the phylogenic trees database with a complex tree user-build motif including duplication and speciation events. Alternitavely you can use a command-line version of FamFetch. If you are only intersted in animal genomes, we recommand the HOMOLENS database for which precalculated othologous animal genes are available.

Acces to HOVERGEN

You can query the database on thispage or via several access :

• the PBIL web applications : WWW-Query, Quick-Search, Cross-Taxa
• the FamFetch client-server application, allowing orthologous and paralogous genes selection
• the QueryWin and Raa_Query, two client-server applications (via sockets)
• the seqinR R package (via sockets)

Contents

Data Origin

The database itself contains all vertebrate protein sequences from the UniProt Knowledgebase (Swiss-Prot and TrEMBL) with some annotation modifications. It contains also all the corresponding nucleotide sequences in EMBL. Homologous proteins are classified into families and multiple alignments and phylogenetic trees are computed for each family. Sequences and related information have been structured in an ACNUC database.

Sequences, Families, Alignments, Phylogenetic trees

Number of proteins	415,383
Number of CDS	613,473
Number of genomic sequences	541,405
Number of families (at least 2 sequences)	16,673
Number of orphans	24,234 (5%)
Number of protein sequences associated to a family	311,647 (75%)
Number of unclassified partial protein sequences	79,502 (19%)

Alignments for families containing 2 to 1000 sequences have been calculated with MUSCLE

Phylogenetic trees for families containing 3 to 1000 sequences have been calculated with PHYML V3.0 (SH-like branch supports, substitution model = JTT, estimated proportion of invariable sites, 4 categories, estimated gamma, initial tree with BIONJ, "NNI" and "SPR" topology exploration) on conserved blocks of the alignments selected with GBLOCKS.

Paralogy/Orthology Events Assignment Phylogenetic trees of each gene family are analysed using RapMasse to assign duplication or speciation event to each node by comparison with the species tree.

HOVERGEN is now available. You can make requests on the protein and the genome data via our web server or via the socket server.

Server mirroring

You don't need to install the server itself to have HOVERGEN running on your computer as the client is enough for that purpose. On the other hand you may want to set-up your own server in a way to speed up your database access and to propose that service to potential users in your geographic area. Installation instructions can be found at http://pbil.univ-lyon1.fr/databases/acnuc/localinstall.html

The whole database is available from our FTP server at URL: ftp://pbil.univ-lyon1.fr/pub/hovergen/ Note that it is much more efficient to use a dedicated FTP client to download the database rather than an Internet Web browser.

Important note:
Some entries such as those found in HOVERGEN are copyrighted since they are initailly produced by EBI,SIB,NCBI,JGI,TIGER. There are no restrictions on its use by non-profit institutions as long as its content is in no way modified. Usage by and for commercial entities requires a license agreement.

Family Building

To build the families we perform a similarity search of all the proteins against each other with BLASTP2. For this purpose, we use the BLOSUM62 similarity matrix and a threshold of 10-4 for E-values. Low complexity sequences are filtered with SEG. Then, the results are processed this way:

• For each pair of sequences, Homologous Segment Pairs (HSPs) that are not compatible with a global alignment are removed
• Two sequences in a pair are included in the same family if:
  • The remaining HSPs cover at least 80% of the proteins length.
  • Their similarity is greater or equal to 50% (two amino-acids are considered similar if the BLOSUM62 similarity score is positive)
• We use simple transitive links to build our families. If a pair of sequences named A + B and a pair of sequences B + C fulfill the conditions listed above, then A, B and C are integrated in the same family, this even if the pair A + C does not fulfill these conditions.

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Sequence Annotations

Family annotation

Protein sequences: we add for each entry a line in the CC field that gives the number of the family the sequence belongs to:

CC   -!- GENE_FAMILY: HBG017522.

Genome sequence: we add for each coding sequence a qualifier that gives the number of the family the gene belongs to:

FT                   /gene_family="HBG017522"

This number is incorporated in the keywords associated to the corresponding entry in the ACNUC database structure. Due to that fact it is possible to retrieve all the sequences associated to a family with this number when using the retrieval system Query or the on-line version WWW-Query.

GC content and intron information annotations

We include in the the genomic sequneces the GC content of each coding sequence:

FT                   /%(C+G)="CG<35%"
FT                   /note="C+G content in third codon positions = 31.4 % "

It is thus possible to select sequences according to its GC content.

We also include in genmoic sequences descriptions of non-coding regions:

• INT_INT: internals introns (i.e. within CDS)
• 5'INT: introns in 5'UTR
• 3'INT: introns in 3'UTR
• 5'NCR: 5' non-coding region
• 3'NCR: 3' non-coding region

For example:

FT   3'ncr           2278..2368

These subsequences can be selected and extracted from the database in the same way as CDS, using WWW-Query (see Help).

Contact and reference

If you encounter some problems when installing or using HOVERGEN, please contact Laurent Duret or Simon Penel Also we welcome any comments or suggestions on the database and/or its interface.

Acknowledgements

Calculations have been done at the IN2P3 Computing Center.

Licence

HOVERGEN Database
Copyright 2005 CNRS
Authors: Laurent Duret,Manolo Gouy, Simon Penel, Guy Perriere

This database is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
A copy of the GNU General Public License is available at ftp://pbil.univ-lyon1.fr/pub/hogenom and http://www.gnu.org/licenses/.

References

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If you use families from HOVERGEN please cite :

• Duret, L., Perrière, G. and Gouy, M. (1999) "HOVERGEN: database and software for comparative analysis of homologous vertebrate genes". In Bioinformatics Databases and Systems, Letovsky, S. (ed.), Kluwer Academic Publishers, Boston, pp. 13-29.
  
• Dufayard J.F., Duret L., Penel S., Gouy M., Rechenmann F. and Perrière G. (2005) "Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases" Bioinformatics, vol. 21 pp.2596-2603