Useful Web Sites for Part 2
Sequence Alignments
Chapter 4: Producing and Analyzing Sequence Alignments
Chapter 5: Pairwise Sequence Alignment and Database Searching
Chapter 6: Patterns, Profiles and Multiple Alignments
Sequence formats:
There are many different ways of representing individual sequences and multiple aligned sequences in text files.
An excellent introductory guide with examples is available on an EBI help page
The EMBOSS suite of analysis programs also contains a guide to alternative formats and their inter-conversion
Many sequence analysis programs can read and write several formats, but occasionally it is necessary to convert between formats
in order to use an application. Two free programs available are:
Readseq – web server with download link
SeqVerter
Sequence and sequence alignment databases:
The following are the sites with general information about specific databases:
Nucleotide sequence databases:
GenBank is a sequence database, including specialised sections such as dbEST for expressed sequence tags.
EMBL Nucleotide Sequence database
Protein sequence databases:
UniProt is a protein sequence resource, which contains specialised sections including UniProtKB/Swiss-Prot (also known as
Swiss-Prot) and UniProtKB/TrEMBL (also known as TrEMBL)
Sequence pattern and motif databases:
BLOCKS database of aligned protein sequences
Domain and protein family databases:
InterPro database of aligned sequences of protein families, domains and functional sites
Prodom comprehensive set of protein domain families as aligned sequences
Protein sequence patterns databases:
Prosite
Protein sequence profile HMM databases:
Pfam
Multiple alignment databases:
FSSP (families of structurally similar proteins)
Homologous Structure Alignment Database (HOMSTRAD)
To access the data, use either of the following sites:
European Bioinformatics Institute (EBI)
National Center for Biotechnology Information (NCBI) Tools for Data Mining
Other useful information:
Coping with limited data:
Dirichlet mixtures and other prior distributions
Multiple alignment test databases:
BAliBASE versions 1 and 2; version 3
Oxbench
Protein Reference Alignment Benchmark (PREFAB)
Programs
Sequence format conversion programs:
SeqVerter™
Database search and pairwise alignment programs:
Dotter
FASTA
NCBI BLAST which includes PSI-BLAST
FSA-BLAST
WU BLAST 2.0
Low complexity sequence mask programs:
DUST and DustMasker
SEG
Very long sequence and genome alignment programs:
BLASTZ
BLAT
CHAOS
MUMMER3
LAGAN and associated programs
SSAHA
Multiple sequence alignment programs:
ClustalW
DIALIGN
MAFFT
MSA
MUSCLE
ProbCons
SAGA
SATCHMO is implemented in LOBSTER
T-COFFEE
An extensive listing is available at http://en.wikipedia.org/wiki/Sequence_alignment_software.
Hidden Markov model programs:
Sequence Alignment and Modeling System (SAM)
HMMER
Alignment visualisation and formatting programs:
CINEMA
PFAAT
WebLogo
Programs for aligning multiple alignments:
prof_sim
COMPASS
Programs for aligning HMMS:
COACH is implemented in LOBSTER
HHsearch
Programs for identifying common patterns in a set of sequences:
Gibbs
MEME
PRATT
Programs for finding known patterns in a sequence:
MAST
ps_scan is a perl script to search for PROSITE patterns
Web servers
Apart from the web pages at the major bioinformatics resource sites listed on the web page for Part 1, which offer access to many
alignment programs, the following web sites provide on-line access to sequence analysis programs:
William R. Pearson’s FASTA programs at the University of Virginia
PRRN
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Datafiles used for Chapter 4 examples
Files will be found in the archive ‘Part 2 Sequence Alignments datafiles.zip’.
Breast cancer susceptibility gene protein BRCA2 sequences Fig 4.3 BRCA2.seq
A cAMP-dependent protein kinase and related PI3-kinase p110 sequences Fig 4.5, 4.7, cAMPKinase.seq,
4.10, 4.12-4.13, MultipleKinaseSequences.seq
4.15
Five SH2 domains Fig 4.11 SH2domain.seq
Human prion precursor protein (PrP) Fig 4.14, 4.18 PrionProtein.seq
