Short specialist reviews are topical articles similar in style to Nature News & Views articles. These are focused on a particular topic or method and may reflect an author's opinion rather than the accepted consensus in the field. About 1000 - 2000 words (1.5-3 pages) each.

The section where we appear

Protomics

Proteome families

Pfam

Not method based !

Introduction to Pfam

Why study domains

Pfam – outline to how it works

Mention Pfam-Bs

Number of domains

Sequence coverage

Number of domains with structure

Searching Genomes

Genome annotation using pfam

Comapring Genomes

Genome Coverage – How well are we doing....

Domain:Domain Interactions ?

Pfam 2002 Introduction

Pfam is a manually curated collection of protein families available via the web and in flat file form (1). Genome projects, including both

the human and fly, have used Pfam extensively for large scale functional annotation of genomic data (2,3). The multiple sequence

alignments around which Pfam families are built are important tools for understanding protein structure and function, and form the basis

for techniques such as secondary structure prediction, fold recognition, phylogenetic analysis and mutation design. The latest version of

Pfam (6.6) contains 3071 families that have matches to 69% of sequences and cover 49% of residues in the sequence database.

Each curated family in Pfam is represented by a seed and full alignment. The seed contains representative members of the family, while

the full alignment contains all members of the family as detected with a profile hidden Markov model (HMM) constructed from the seed

alignment using the HMMER2 software (http://hmmer.wustl.edu/). Full alignments can be large with the top 20 families now each

containing over 2500 sequences. The majority of known protein sequences come from just a few thousand protein families. However, in

an effort to be comprehensive, the curated families in Pfam-A are augmented by Pfam-B, an automatically generated supplement derived from the PRODOM database (4).

Pfam is available at four locations around the world, each providing a core set of functionality for accessing each family. Pfam is available in Europe on the World Wide Web at

http://www.sanger.ac.uk/Software/Pfam/ (UK), http://www.cgb.ki.se/Pfam/ (Sweden) and http://pfam.jouy.inra.fr/ (France), and in the US at http://pfam.wustl.edu/. Documentation on the

content and use of Pfam is available via the web. The web sites described above contain documentation on Pfam alignments, mark-up and family annotation. The alignments in Pfam are in

Stockholm format, which is described in detail at http://www.cgb.ki.se/cgb/groups/sonnhammer/Stockholm.html, and the HMMER software is documented at http://hmmer.wustl.edu/.

Pfam 2000 introduction

Pfam is a database of protein domain families. Pfam contains curated multiple sequence alignments for each family, as well as profile hidden

Markov models (profile HMMs) for finding these domains in new sequences. Pfam contains functional annotation, literature references and

database links for each family. There are two multiple alignments for each Pfam family, the seed alignment that contains a relatively small

number of representative members of the family and the full alignment that contains all members in the database that can be detected. All

alignments use sequences taken from pfamseq, which is a non-redundant protein set composed of SWISS-PROT and SP-TrEMBL. The profile

HMM is built from the seed alignment using the HMMER package (see http://hmmer.wustl.edu/ ), which is then used to search the pfamseq

sequence database. All the matches found above the curated thresholds are aligned using the profile HMM to make the full alignment. The

largest full alignment in Pfam, for the HIV GP120 glycoprotein, has >16 000 members, yet the seed alignment only has 24 representative

members. The latest version of Pfam (4.3) contains 1815 families that have matches to 63% of sequences, covering 45% of residues in the sequence database.

One of the main goals of Pfam was to aid the annotation of the Caenorhabditis elegans genome (1). Traditional approaches to large scale sequence annotation use a pairwise sequence

comparison method such as BLAST (2) to find similarity to proteins of known function. Annotations are then transferred from the protein of known function to the predicted protein. The

pairwise similarity search does not give a clear indication of the domain structure of the proteins. Mistakes in annotation can result from not considering the domain organisation of proteins

(3). For example a protein may be misannotated as an enzyme when the similarity is only to a regulatory domain. Since its inception, Pfam has been developed to provide broad support for

automated protein sequence classification and annotation. During the last year there have been significant changes and extensions to Pfam, which further this role.

Introduction from 2004 paper

Pfam is a comprehensive collection of protein domains and families, with a range of well-established uses including genome annotation.

Each family in Pfam is represented by two multiple sequence alignments and two profile-Hidden Markov Models (profile-HMMs). The

functionality, use and philosophy of Pfam have been discussed in previous publications (1,2) and will not be discussed at length here. In the

following sections we describe the most important improvements that have been made to the database in the past 2 years.

Genome stuff from 2000 paper

An important goal of Pfam is to enable rapid automatic classification of predicted proteins into protein domain families. Pfam is used around the

world as an aid to genomic annotation in one of two ways: (i) Pfam can be used to annotate protein translations using the HMMer software; or

(ii) Pfam can be used to predict genes and annotate genomic DNA using the Wise2 package.

Although Pfam's coverage across the sequence databases is high (63%), we know that these databases are biased towards some protein

families and organisms. Therefore it is useful to know what fraction of protein sequences in whole genome sequencing projects are annotated by

Pfam analysis. Table 1 shows a summary of a Pfam/HMMER analysis of the predicted proteins from five representative genomes: the bacteria

Escherichia coli and Rickettsia prowazekii, the nematode Caenorhabditis elegans, the yeast Saccharomyces cerevisiae and the archaeon

Methanococcus jannaschii. Pfam identifies domains in 40-50% of the proteins in each genome, except for the archaeal M.jannaschii genome where the fraction is somewhat lower (33%).

This compares favourably to the fraction of proteins that can be annotated by standard pair-wise BLAST analysis: for example, the worm genome project reported that ~42% of worm

proteins had an informative BLAST similarity to a non-nematode protein (11).

Pfam: A Protein Family Database

Introduction

Genome Discussion

Pfam was orignially set up to aid the annotation of the Caenorhabditis elegans genome (1). More recently, Pfam based annotations have been applied to many genome projects, including both the human and fly. The coverage of Pfam accros the sequence databases is high, but the coverage of Pfam across whole genomes can differes greatly. Figure X demonstrate what fraction of protein sequences are represented in Pfam from a selection of representative genomes. In all of the examples shown, the sequence coverage is always greater than 60%, but in the case of E.coli, exceeds 80%. The amino acid coverage also varies considerably. Such coverage can be as low as 34.8% for yeast, yet as high as 62.2% in E.coli. These differences reflect the bias.....

Nevertheless, profile HMM searches compare very favourably to standard pair-wise BLAST analysis.

As more an more genomes become completed, it is interesting and infomative to identify which families are specfic

Proteomics

2004-03-25T11:52:12