Sage-Tips

What is PROSITE used for?

PROSITE, a protein domain database for functional characterization and annotation. PROSITE is a protein database. It consists of entries describing the protein families, domains and functional sites as well as amino acid patterns and profiles in them.

What are PROSITE patterns?

PROSITE patterns are short sequence motifs, while PROSITE profiles are position specific score matrices. Profiles characterize protein domains over their entire length, and they are more sensitive than patterns. Profiles and patterns have complementary qualities.

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 is PROSITE Expasy?

PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them [More… / References / Commercial users ].

Is PROSITE secondary database?

PROSITE and PRINTS are the only manually annotated secondary databases. The print is a diagnostic collection of protein fingerprints.

How do you reference a PROSITE?

If you want to refer to the PROSITE methodology please cite: Sigrist C.J.A., Cerutti L., Hulo N., Gattiker A., Falquet L., Pagni M., Bairoch A., Bucher P. PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform.

What type of database is Pfam?

curated protein families
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.

Which database of Pfam contains high quality data?

UniProtKB coverage Pfam uses UniProtKB as its reference sequence database. Between Pfam releases 24.0 and 26.0, UniProtKB has increased in size by 69\% (9.4 million sequences in UniProtKB in August 2009 versus 15.9 million sequences in June 2011).

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 are bioinformatics prints?

From Wikipedia, the free encyclopedia. In molecular biology, the PRINTS database is a collection of so-called “fingerprints”: it provides both a detailed annotation resource for protein families, and a diagnostic tool for newly determined sequences.

Is PDB a primary database?

PDB is a primary protein structure database. It is a crystallographic database for the three-dimensional structure of large biological molecules, such as proteins.

Is Prosite secondary database?

What is a Pfam profile HMM?

Each Pfam profile HMM represents a protein family or domain. By searching a protein sequence against the Pfam library of profile HMMs, you can determine which domains it carries i.e. its domain architecture. Pfam can also be used to analyse proteomes and questions of more complex domain architectures.

Why is the Pfam website not showing the match to family B?

Occasionally, the same sequence region has a significant match to another family (family B) in the same clan. In this situation, the Pfam website will not show the match to family B as it is present in the seed alignment of family A. The sequence search will however show the match to family B as the seed alignment information is unknown.

How many times can a Pfam family match a single protein sequence?

A given Pfam family may match a single protein sequence multiple times, if the domain/family is a repeating unit, for example, or when the profile HMM matches only to short stretches of the sequence but matches several times. In such cases the FASTA file with the full length sequences will contain multiple copies of the same sequence.

What is a clan Pfam?

Some of the Pfam families are grouped into clans. Pfam defines a clan as a collection of families that have arisen from a single evolutionary origin. Evidence of their evolutionary relationship can be in the form of similarity in tertiary structures, or, when structures are not available, from common sequence motifs.