Pfam Domains in GENCODE Genes
Pfam Domains in GENCODE Genes - UCSC Genome Browser
This track shows the high-quality, manually-curated Pfam-A domains found in transcripts located in the GENCODE Genes track by the software HMMER3.
Pfam is now hosted by InterPro
The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).
The Pfam Protein Families Database - PMC
Pfam is a database of protein domain families. Pfam contains curated multiple sequence alignments for each family, as well as profile hidden Markov models ( ...
Pfam: The protein families database in 2021 - Oxford Academic
The other domains encoded in this protein are the Macro domain included in Pfam:PF01661 and SUD-M domain in Pfam:PF11633 that binds single- ...
GENCODE VM23 Track Settings - UCSC Genome Browser
The basic set represents transcripts that GENCODE believes will be useful to the majority of users. The track includes protein-coding genes, non-coding RNA ...
... Pfam database (version 15.0). The hidden Markov models for Pfam protein domains are aligned against the genomic sequence using Halfwise ...
GENCODE: The reference human genome annotation for The ...
The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental ...
GENCODE: producing a reference annotation for ENCODE
The GENCODE consortium was formed to identify and map all protein-coding genes ... The hidden Markov models for Pfam protein domains are aligned ...
Pfam | Cross-referenced databases - UniProt
Database - Pfam · Name. Pfam protein domain database · Servers. www.ebi.ac.uk/interpro · Link type. Explicit · Category. Family and domain databases · DOI ID.
Pfam Based Functional Annotaion - Biostars
It should be emphasized that the use of these databases for homology transfer should be done with caution, as they annotate proteins on a domain ...
Most partial domains in proteins are alignment and annotation artifacts
... domains. Pfam protein domains are often thought of as evolutionarily ... genome assemblies or gene models. We also find that a large ...
APPRIS 2017: principal isoforms for multiple gene sets
... Pfam domains (13) and highly conserved functional residues (14). Information from APPRIS is fed back to the GENCODE manual annotators to ...
Variant Effect Predictor Input form - Ensembl
GENCODE Basic is a subset of the GENCODE gene set, and is intended to provide a simplified, high-quality subset of the GENCODE transcript annotations that will ...
The GENCODE annotation is made by merging the manual gene annotation produced by the Ensembl-Havana team and the Ensembl-genebuild automated gene annotation.
Gene and Gene Predictions, GENCODE Genes V19, Comprehensive ... Pfam domains v28, Pfam-A.hmm, ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases ...
Pfam domain search - CLC Manuals - clcsupport.com
elegans genome. The database is a large collection of multiple sequence alignments that cover 14831 protein domains and protein families as of March 2014. The ...
Gene/Transcript Biotypes in GENCODE & Ensembl
Gene/Transcript Biotypes in GENCODE & Ensembl ; lncRNA, Generic long non-coding RNA biotype that replaced the following biotypes: 3prime_overlapping_ncRNA, ...
Mapping between genome, transcript and protein coordinates
The protein domain is encoded by a sequence spanning exons 2 to 5 of the transcript ENST00000263233. Note that the gene is encoded on the ...
Pfam Domains in RefSeq Genes (adh_short)
Most proteins are composed of one or more conserved functional regions called domains. This track shows the high-quality, manually-curated Pfam- ...
The current version of GENCODE is the default geneset in the Ensembl Genome Browser for human and mouse. The Ensembl data can also be accessed using the ...