What is the main differences of pfam, ProDom and ProSiteProfiles?

Question

[seta]

Hi all friends,

I read about pfam, ProDom and ProSiteProfiles and got that they used for domain homology search. My question is: what are the main differences among these databases? Please clear me with a simple example if it's possible as I'm totally confused about them.

Thanks

Answer 1

[natasha.sernova]

Let's go step by step at first:

Difference Between Pfam And Prosite ?

A: Pfam Based Functional Annotaion

ProDom:

http://prodom.prabi.fr/prodom/current/documentation/help.php

I would read corresponding refernces from this paper:

Why do Sequence Signatures Predict Enzyme Mechanism? Homology versus Chemistry

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4696837/

I enumerated them below:

Finn RD, Bateman A, Clements J, et al. Pfam: the protein families database. Nucleic Acids Res. 2014;42:D222–30. [PMC free article] [PubMed]

http://nar.oxfordjournals.org/content/early/2013/11/26/nar.gkt1223.full.pdf+html

"ABSTRACT Pfam, available via servers in the UK (http://pfam. sanger.ac.uk/) and the USA (http://pfam.janelia. org/), is a widely used database of protein families, containing 14 831 manually curated entries in the current release, version 27.0. Since the last update article 2 years ago, we have generated 1182 new families and maintained sequence coverage of the UniProt Knowledgebase (UniProtKB) at nearly 80%, despite a 50% increase in the size of the underlying sequence database. Since our 2012 article describing Pfam, we have also undertaken a com- prehensive review of the features that are provided by Pfam over and above the basic family data. For each feature, we determined the relevance, computational burden, usage statistics and the functionality of the feature in a website context. As a consequence of this review, we have removed some features, enhanced others and developed new ones to meet the changing demands of compu- tational biology. Here, we describe the changes to Pfam content. Notably, we now provide family align- ments based on four different representative proteome sequence data sets and a new interactive DNA search interface. We also discuss the mapping between Pfam and known 3D structures."

Bru C, Courcelle E, Carrere S, Beausse Y, Dalmar S, Kahn D. The ProDom database of protein domain families: more emphasis on 3D. Nucleic Acids Res. 2005;33:D212–5. [PMC free article] [PubMed]

https://www.ncbi.nlm.nih.gov/pubmed/15608179

"Abstract

ProDom is a comprehensive database of protein domain families generated from the global comparison of all available protein sequences. Recent improvements include the use of three-dimensional (3D) information from the SCOP database; a completely redesigned web interface (http://www.toulouse.inra.fr/prodom.html); visualization of ProDom domains on 3D structures; coupling of ProDom analysis with the Geno3D homology modelling server; Bayesian inference of evolutionary scenarios for ProDom families. In addition, we have developed ProDom-SG, a ProDom-based server dedicated to the selection of candidate proteins for structural genomics."

Sigrist CJA, de Castro E, Cerutti L, et al. New and continuing developments at PROSITE. Nucleic Acids Res. 2013;41:D344–7. [PMC free article] [PubMed]

http://nar.oxfordjournals.org/content/early/2012/11/16/nar.gks1067.full.pdf+html

"ABSTRACT PROSITE (http://prosite.expasy.org/) consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. It is comple mented by ProRule a collection of rules, which in creases the discriminatory power of these profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. PROSITE signatures, together with ProRule, are used for the annotation of domains and features of UniProtKB/Swiss-Prot entries. Here, we describe recent developments that allow users to perform whole-proteome annotation as well as a number of filtering options that can be combined to perform powerful targeted searches for biological discovery. The latest version of PROSITE (release 20.85, of 30 August 2012) contains 1308 patterns, 1039 profiles and 1041 ProRules."

Abstracts allow to make some conclusions.

ProDom is relatively old.

Pfam is manually curated.

Prosite use its own rules in addition.

I would use PFam if you need to choose a single database.

Read these three articles if you need some additional details.

As a conclusion see the very bottom of the page below (there are all the program-links together):

http://pfam.xfam.org/help#tabview=tab3