hamap.expasy.org

HAMAP home

High-quality Automated and Manual Annotation of Proteins. HAMAP is a system for the classification and annotation of protein sequences. It consists of a collection of manually curated family profiles for protein classification, and associated, manually created annotation rules. That specify annotations that apply to family members. HAMAP is used to annotate protein records in UniProtKB via UniProt's automatic annotation pipeline. For UniProt release 2018 03. Number of family profiles. Back to the Top.

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HAMAP home | hamap.expasy.org Reviews

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High-quality Automated and Manual Annotation of Proteins. HAMAP is a system for the classification and annotation of protein sequences. It consists of a collection of manually curated family profiles for protein classification, and associated, manually created annotation rules. That specify annotations that apply to family members. HAMAP is used to annotate protein records in UniProtKB via UniProt's automatic annotation pipeline. For UniProt release 2018 03. Number of family profiles. Back to the Top.

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HAMAP home | hamap.expasy.org Reviews

https://hamap.expasy.org

High-quality Automated and Manual Annotation of Proteins. HAMAP is a system for the classification and annotation of protein sequences. It consists of a collection of manually curated family profiles for protein classification, and associated, manually created annotation rules. That specify annotations that apply to family members. HAMAP is used to annotate protein records in UniProtKB via UniProt's automatic annotation pipeline. For UniProt release 2018 03. Number of family profiles. Back to the Top.

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hamap.expasy.org

1

HAMAP documents

https://hamap.expasy.org/hamap_details.html

HAMAP stands for H. Sometimes, we need to use a somewhat different approach for the annotation of large and complex paralogous families (. ABC transporters). For these, stringent profiles are required to distinguish between functional subfamilies regarding the transported substrate. For ABC transporters, manually built PROSITE profiles are used to assign family membership and there are no seed alignments. Where you can browse, search and view the HAMAP profiles and annotation rules. General information a...

2

HAMAP proteomes

https://hamap.expasy.org/proteomes.html

The proteome pages provide curated information on all bacterial and archaeal UniProtKB reference proteomes. UP000008458 ACIHW Acidianus hospitalis (strain W1). UP000000346 ACIS3 Acidilobus saccharovorans (strain DSM 16705 / JCM 18335 / VKM B-2471 / 345-15). UP000050301 / Acidiplasma cupricumulans. UP000001400 ACIB4 Aciduliprofundum boonei (strain DSM 19572 / T469). UP000002518 AERPE Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1). UP000031777 / archaeon GW2011 AR10. UP0000...

3

HAMAP Documentation

https://hamap.expasy.org/hamap_doc.html

User Manual for the Web View. Standard operating procedure (SOP) for HAMAP family profiles creation. User Manual for the Web View. Standard operating procedure (SOP) for HAMAP annotation rule creation. HAMAP in 2015: updates to the protein family classification and annotation system. Nucleic Acids Res. 43:D1064-D1070(2015). HAMAP in 2013, new developments in the protein family classification and annotation system. Nucleic Acids Res. 41:D584-D589(2013). Nucleic Acids Res. 37:D471-D478(2009).

4

HAMAP-Scan

https://hamap.expasy.org/hamap_scan.html

Classify (and annotate) your own protein sequences by using the collection of HAMAP family profiles and annotation rules [ help. Retrieve results of a previous scan. STEP 1 - Enter PROTEIN sequences. Enter PROTEIN sequences (max. 1'000). Upload a file (up to 100'000 sequences). Accessions e.g. Q8ZHG0 or identifiers e.g. AGUA YERPE. Amino acid sequences in FASTA format. Upload a file containing your PROTEIN sequences in FASTA format. STEP 2 - Choose 'Scan' or 'Scan and Annotate'. STEP 3 - Submit your job.

5

Annotation rule MF_00191

https://hamap.expasy.org/unirule/MF_00191

Annotation rule MF 00191. General rule information [? 29-MAR-2016 (Last updated, Version 40). ISPH ECOLI); O67625. ISPH AQUAE); Q55643. ISPH SYNY3): [ Recover all. HAMAP; MF 00191 (Get profile general information and statistics). Identifier, protein and gene names [? Full=4-hydroxy-3-methylbut-2-enyl diphosphate reductase;. EC= 117.7.4. Converts 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Binds 1 [3Fe-4S] cluster per subunit.

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interprodb.blogspot.com

InterPro database blog: A new InterPro member database

http://interprodb.blogspot.com/2016/06/a-new-interpro-member-database.html

Thursday, 9 June 2016. A new InterPro member database. We are pleased to announce that the NCBI Conserved Domain Database ( CDD. Has joined the InterPro. Consortium as a member database, and has begun to be integrated into the resource. This is the first new member database to be integrated into InterPro since HAMAP. Was included, back in 2009. As you can see, it has been 7 years since a new database has been added, and this is a first for the current InterPro team. What does CDD bring? CDD entry cd00770...

seqdepot.net

SeqDepot

http://seqdepot.net/stats

Ulrich, L.E. and Zhulin, I.B. Bioinformatics (2014). 8,934,788,107. Transmembrane regions ( DAS. Low complexity regions (seg). Signal peptides ( SignalP. Subcellular locations ( TargetP. Transmembrane regions ( TMHMM. Developed and maintained by Luke Ulrich.

interprodb.blogspot.com

InterPro database blog: June 2016

http://interprodb.blogspot.com/2016_06_01_archive.html

Thursday, 9 June 2016. A new InterPro member database. We are pleased to announce that the NCBI Conserved Domain Database ( CDD. Has joined the InterPro. Consortium as a member database, and has begun to be integrated into the resource. This is the first new member database to be integrated into InterPro since HAMAP. Was included, back in 2009. As you can see, it has been 7 years since a new database has been added, and this is a first for the current InterPro team. What does CDD bring? CDD entry cd00770...

web.expasy.org

UniProtKB/Swiss-Prot

http://web.expasy.org/docs/swiss-prot_guideline.html

UniProtKB/Swiss-Prot is the manually annotated and reviewed section of the UniProt Knowledgebase (UniProtKB). It is a high quality annotated and non-redundant protein sequence database, which brings together experimental results, computed features and scientific conclusions. Since 2002, it is maintained by the UniProt consortium. And is accessible via the UniProt website. List of UniProtKB/Swiss-Prot (reviewed) entries. Download - UniProt FTP sites. How do we manually annotate a UniProtKB entry?

seqdepot.net

SeqDepot

http://seqdepot.net/download

Ulrich, L.E. and Zhulin, I.B. Bioinformatics (2014). SeqDepot Mongo Database (not currently available for download). Database - all sequences and precomputed features. Excludes all secondary indices (e.g. cross-references). Perl script for performing common tasks. Works with FASTA data or a list of Aseq IDs, GI, UniProt, PDB, or MD5 digests. Produce domain architecture images (PNG or SVG). Easily incorporate into processing pipelines. Encoded data for any (or all) of the following:. Python 3.x module.

expasy.org

ExPASy: SIB Bioinformatics Resource Portal - Categories

http://www.expasy.org/proteomics/protein_sequences_and_identification

Query within a category:. Query a specific database:. Protein sequences and identification. Sequence sites, features and motifs. No support from the ExPASy Team). Bull; functional information on proteins • [more]. Bull; protein sequence database • [more]. Bull; portal to viral UniProtKB entries • [more]. Bull; ViralZone is a web resource for all viral genus and families, providing general molecular and epidemiological informations, along with virion and genome figures. Each virus or family page gives...

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hamap.expasy.org

HAMAP home

High-quality Automated and Manual Annotation of Proteins. HAMAP is a system for the classification and annotation of protein sequences. It consists of a collection of manually curated family profiles for protein classification, and associated, manually created annotation rules. That specify annotations that apply to family members. HAMAP is used to annotate protein records in UniProtKB via UniProt's automatic annotation pipeline. For UniProt release 2018 03. Number of family profiles. Back to the Top.

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Accès à la boutique. Rapport d’activités HAMAP 2013. Rapport d’activités HAMAP 2012. Rapport d’activités HAMAP 2011. Rapport d’activités HAMAP 2010. Découvrez notre boutique 100% HAMAP proposant des objets de collections dont la vente financera nos actions. Http:/ boutique.hamap.org/. Madame, Monsieur,. FOTOVAR vous invite à nouveau à venir exprimer votre talent et exposer vos plus belles photos, vos meilleures créations, les 19 et 20 septembre 2015 à DRAGUIGNAN. Exposition de photos sous-marines. L’ONG ...

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