What does Pfam stand for?
PFAM
| Acronym | Definition |
|---|---|
| PFAM | Protein Families (database) |
| PFAM | Processing and Fabrication of Advanced Materials (symposium) |
| PFAM | Policy and Financial Analysis Model (US HUD) |
What is Pfam-A and Pfam B?
The use of representative seed alignments for Pfam-A families allows efficient and sustainable manual curation of alignments and annotation, while the automatic generation of full alignments and Pfam-B clusters ensures that Pfam is a comprehensive classification of protein families that scales effectively with the …
Why do we use Pfam?
The general purpose of the Pfam database is to provide a complete and accurate classification of protein families and domains. Originally, the rationale behind creating the database was to have a semi-automated method of curating information on known protein families to improve the efficiency of annotating genomes.
How do I find Pfam?
You can perform the same search from anywhere within the Pfam site, using the keyword search box at the top right-hand side of every page.
What type of database is Pfam?
Pfam is a database of curated protein families, each of which is defined by two alignments and a profile hidden Markov model (HMM). Profile HMMs are probabilistic models used for the statistical inference of homology (1,2) built from an aligned set of curator-defined family-representative sequences.
What is E value Pfam?
The E-value (expectation value) is the number of hits that would be expected to have a score equal to or better than this value, by chance alone. This means that a good E-value which gives a confident prediction is much less than 1. E-values around 1 is what is expected by chance.
What is a Pfam seed alignment?
Each Pfam family, often referred to as a Pfam-A entry, consists of a curated seed alignment containing a small set of representative members of the family, profile hidden Markov models (profile HMMs) built from the seed alignment, and an automatically generated full alignment, which contains all detectable protein …
What type of alignment does Pfam do?
What is PDB used for?
Through an internet information portal and downloadable data archive, the PDB provides access to 3D structure data for large biological molecules (proteins, DNA, and RNA). These are the molecules of life, found in all organisms on the planet.
Is Pfam a secondary database?
Two of the most popular secondary databases recognise conserved protein domains within a protein sequence. These databases are Pfam and Interpro and they are hosted by EMBL-EBI.
What is bit-score in Pfam?
The bit-score is a measure of how well a sequence matches the profile HMM (i.e. if the sequence is homologous to the model) and is independent of the size of the database.
Is Pfam-a secondary database?
How are proteins represented in the Pfam database?
The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs) . More… Proteins are generally composed of one or more functional regions, commonly termed domains. Different combinations of domains give rise to the diverse range of proteins found in nature.
Why are domains of unknown function named Pfam?
Domains of unknown function (DUFs) represent a growing fraction of the Pfam database. The families are so named because they have been found to be conserved across species, but perform an unknown role. Each newly added DUF is named in order of addition.
What does Pfam stand for in Football Union?
For the Malaysian football labor union that used the acronym PFAM, see Professional Footballers Association of Malaysia. The Pfam database provides alignments and hidden Markov models for protein domains. Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models.
Which is the most recent version of Pfam?
Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The most recent version, Pfam 34.0, was released in March 2021 and contains 19,179 families.