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HAMAP specifications


Unique identifier OMICS_26378
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes


  • person_outline Alan Bridge

Additional information


Publications for HAMAP

HAMAP citations


Toward Understanding Phage:Host Interactions in the Rumen; Complete Genome Sequences of Lytic Phages Infecting Rumen Bacteria

Front Microbiol
PMCID: 5723332
PMID: 29259581
DOI: 10.3389/fmicb.2017.02340

[…] rotein model databases Pfam-A (release 30.0), TIGRfam 15.0, and COG2014 (Haft et al., ; Galperin et al., ; Finn et al., ), and Prokka version 1.1 using the protein model databases Pfam, COG clusters, HAMAP, Resfams, TIGRfam 15.0, and dbCAN v4 (Yin et al., ; Haft et al., ; Galperin et al., ; Gibson et al., ; Pedruzzi et al., ; Finn et al., ). The putative function of predicted ORF's were also assig […]


Genomic assessment in Lactobacillus plantarum links the butyrogenic pathway with glutamine metabolism

Sci Rep
PMCID: 5698307
PMID: 29162929
DOI: 10.1038/s41598-017-16186-8

[…] ters, with the exception of sequence E-value (e−10) as well as with InterproScan (ver. 5.18-57.0;) against all the available databases (ProSiteProfiles-20.119), PANTHER-10.0, Coils-2.2.1, PIRSF-3.01, Hamap-201511.02, Pfam-29.0, ProSitePatterns-20.119, SUPERFAMILY-1.75, ProDom-2006.1, SMART-7.1, Gene3D-3.5.0 and TIGRFAM-15.0. Additional information on metabolic pathways was highlighted using the KA […]


Chemosensing of honeybee parasite, Varroa destructor: Transcriptomic analysis

Sci Rep
PMCID: 5638865
PMID: 29026097
DOI: 10.1038/s41598-017-13167-9

[…] characteristic for each family using Blast2GO with default parameters. We used InterproScan with the following domain search: BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, HAMAP, PatternScan, SuperFamily, SignalPHMM, TMHMM, HMMPanther, Gene3D, Phobius, Coils, CDD and SFLD. […]


The single cyclic nucleotide specific phosphodiesterase of the intestinal parasite Giardia lamblia represents a potential drug target

PLoS Negl Trop Dis
PMCID: 5617230
PMID: 28915270
DOI: 10.1371/journal.pntd.0005891
call_split See protocol

[…] , two HMMs were created: (a) by using the twenty most diverse members of the NCBI CDD family PRK11148 (http://www.ncbi.nlm.nih.gov/cdd); (b) by using a seed alignment of 49 sequences contained in the HAMAP profile MF_00905 []. All hits above the significance threshold (e < 0.0001) were analyzed manually.Sequence patterns searches were done with the programs fuzzpro and patmatdb (EMBOSS software pa […]


BrEPS 2.0: Optimization of sequence pattern prediction for enzyme annotation

PLoS One
PMCID: 5531587
PMID: 28750104
DOI: 10.1371/journal.pone.0182216

[…] rovide pattern based genome annotation. ProDom [] and Pfam [] provide patterns related to protein domains while other databases focus on patterns to categorize proteins into families, like PRINTS [], HAMAP [] and PRIAM []. InterPro is a database classifying protein sequences into families predicting important domains and sites []. InterPro incorporates 14 different databases, including those menti […]


Genome wide signatures of complex introgression and adaptive evolution in the big cats

Sci Adv
PMCID: 5517113
PMID: 28776029
DOI: 10.1126/sciadv.1700299

[…] sequence was submitted in FASTA format. Matches were then calculated against all of the required member database signatures (BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, HAMAP, PatternScan, SuperFamily, SignalPHMM, TMHMM, HMMPanther, Gene3D, Phobius, and Coils), and the results were output in TSV (a simple tab-delimited file) format. The InterProScan5 approach was abl […]


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HAMAP institution(s)
Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, Geneva, Switzerland; Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland; Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland; Department of Biochemistry, University of Geneva, Geneva, Switzerland
HAMAP funding source(s)
Supported by the Swiss Federal Government through the State Secretariat for Education, Research and Innovation; National Institutes of Health [U41HG006104]; and Swiss National Science Foundation [JRP09 and JRP13].

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