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Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. [ 1 ] [ 2 ] [ 3 ] The latest version of Pfam, 37.0, was released in June 2024 and contains 21,979 families. [ 4 ]
Stockholm format is a multiple sequence alignment format used by Pfam, Rfam and Dfam, to disseminate protein, RNA and DNA sequence alignments. [1] [2] [3] The alignment editors Ralee, [4] Belvu and Jalview support Stockholm format as do the probabilistic database search tools, Infernal and HMMER, and the phylogenetic analysis tool Xrate.
PFAM was inactive for a few years until it was reactivated in 2013, with Hairuddin Omar elected as president of the association. [4] For the 2021-2023 session, Safee Sali led the organization and was assisted by Razman Roslan as Vice President. PFAM is vocal about welfares of football players in Malaysia, whether still active of retired. [5]
This is template for a protein family/domain as defined in biological databases such as Pfam. Template parameters [Edit template data] Parameter Description Type Status Symbol Symbol no description Line optional Name Name no description Line optional Image image fill in "NONE" if not needed to suppress the tracking category File optional Width width Width for image String optional Caption ...
TIGRFAMs is a database of protein families designed to support manual and automated genome annotation. [1] [2] [3] Each entry includes a multiple sequence alignment and hidden Markov model (HMM) built from the alignment. Sequences that score above the defined cutoffs of a given TIGRFAMs HMM are assigned to that protein family and may be ...
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Rfam is designed to be similar to the Pfam database for annotating protein families. Unlike proteins, ncRNAs often have similar secondary structure without sharing much similarity in the primary sequence. Rfam divides ncRNAs into families based on evolution from a common ancestor.
A recent study to understand and improve Pfam coverage of the human proteome [17] showed that five of the ten largest sequence clusters not annotated with Pfam are repeat regions. Alternatively, methods requiring no prior knowledge for the detection of repeated substrings can be based on self-comparison, [ 18 ] [ 19 ] clustering [ 20 ] [ 21 ...