Genome Science (IBB.MB.
501)
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Database search and sequence alignment
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Introduction
– Over the past five decades the use of computers has had a profound
effect on research in the biological sciences
– The amount of information available to researchers in databases,
increases almost exponentially, with biologists and computer scientists
coming together to provide Bioinformatics tools to help extract useful
information from these databases
– The aim of these sessions is to introduce you to the use of some of the
information and software resources available in the public domain
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Searching sequence databases
– Sequence databases exist for nucleic acids, proteins and complex
carbohydrates
– For nucleic acids and proteins the chemical structure is represented as
a string of characters, such as ACCGTA for nucleic acids or DFGIMCR
for proteins
– Database entries include much more information, or annotation, which
contains the biological, bibliographic and administrative context for
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the sequence.
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NA databases
– For nucleic acids, there are three major public domain databases:
– European Nucleotide Archive, from EMBL-EBI
– NCBI (including GenBank (USA))
– DDBJ (DNA DataBank of Japan)
– All exchange information daily, so that they are essentially identical
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Sequence Alignment
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Job Dispatcher ❏50+ tools
Bioinformatics Tools (nucleotide and
protein analysis)
❏Recently added:
❏R2DT
❏SSRAECH2SEQ
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❏GGSEARCH2SE
Q
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Tool Categories
▪ Sequence Format Conversion (sfc)
▪ Protein Function Analysis (pfa)
▪ Sequence Operation (so)
▪ Sequence Statistics (seqstats)
▪ Sequence Translation (st)
▪ RNA Analysis (rna)
▪ Phylogeny (phylogeny)
▪ Pairwise Sequence Alignment (psa)
▪ Multiple Sequence Alignment (msa)
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▪ Sequence Similarity Search (sss)
▪ Emboss Tools (emboss)
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Sequence Format Conversion (sfc)
❏Convert one sequence format to another.
❏EMBOSS Seqret, MView
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Advantages
• No local installation
• Workflows
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Typical Bioinformatics Setup
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How to access tools?
– EBI Service page:
– https://www.ebi.ac.uk/services
– Job dispatcher Tool category page:
– https://www.ebi.ac.uk/Tools/<category>
– Eg: https://www.ebi.ac.uk/Tools/msa (Multiple Sequence Alignment)
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https://www.ebi.ac.uk/services
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Sequence Alignment
– Identify regions of similarity
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Sequence Alignment
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Sequence Alignment
– Match, Mismatch, Gap
– Gap extension penalty
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Sequence alignment
– Similarity and Identity
– Substitution matrix
– https://github.com/kimrutherford/EMBOSS/tree/master/emboss/data
– Alignment score : calculated based on the match/mismatch of residues
using the substitution matrices
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Sequence Alignment Types
PAIRWISE MULTIPLE
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Pairwise Sequence Alignment
– Involves aligning two sequences using a scoring matrix
– Basic of database similarity search
– Dynamic Programming for global alignment : Needleman-Wunsch
algorithm
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– Dynamic programming for local alignment : Smith-Waterman
Algorithm
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Local and Global Alignment
– Global
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– Local
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Pairwise Alignment Tools
https://www.ebi.ac.uk/Tools/psa/
– Needle
– Stretcher
– GGSEARCH2SEQ
– Water
– Matcher
– LALIGN
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– SSEARCH2SEQ
– GeneWISE
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Which tool to use?
– Global Alignment
Needle Stretcher GGSEARCH2SEQ
(big sequences)
– Local Alignment
Water LALIGN Matcher SSEARCH2SE
(big sequences)
Q
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https://www.ebi.ac.uk/Tools/psa/emboss_needle/
Sequence input
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Parameters
Submit! 26
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Things to remember
– Selection of tool
– Choose local/global based on your requirement
– Selection of Matrix
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– Blosum{n} higher value focus on more closely related proteins.
– PAM{n} higher value focuses on more distantly related proteins.
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What is BLAST?
– Basic BLAST search
– What is BLAST?
– The framework of BLAST
– Different BLAST programs
– BLAST databases you can search
– Where can I run BLAST?
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What is BLAST?
• BLAST stands for
Basic Local Alignment Search Tool
• Why BLAST is popular?
- Good balance of sensitivity and speed
- Reliable
- Flexible
• Produce local alignments: short significant stretches of
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similarity, irrespective of where they are in the sequence
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BLAST Programs
The most common BLAST search include five programs:
Program Database (Subject) Query
BLASTN Nucleotide Nucleotide
BLASTP Protein Protein
BLASTX Protein Nt. ➔ Protein
TBLASTN Nt. ➔ Protein Protein
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TBLASTX Nt. ➔ Protein Nt. ➔ Protein
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BLASTN
– BLASTN
– The query is a nucleotide sequence
– The database is a nucleotide database
– No conversion is done on the query or database
– DNA :: DNA homology
– Mapping oligos to a genome
– Annotating genomic DNA with transcriptome data from ESTs
and RNA-Seq
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– Annotating untranslated regions
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BLASTP
– BLASTP
– The query is an amino acid sequence
– The database is an amino acid database
– No conversion is done on the query or database
– Protein :: Protein homology
– Protein function exploration
– Novel gene ➔ make parameters more sensitive
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BLASTX
– BLASTX
– The query is a nucleotide sequence
– The database is an amino acid database
– All six reading frames are translated on the query and used
to search the database
– Coding nucleotide seq :: Protein homology
– Gene finding in genomic DNA
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– Annotating ESTs and transcripts assembled from RNA-Seq
data
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TBLASTN
– TBLASTN
– The query is an amino sequence
– The database is a nucleotide database
– All six frames are translated in the database and searched
with the protein sequence
– Protein :: Coding nucleotide DB homology
– Mapping a protein to a genome
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– Mining ESTs and RNA-Seq data for protein similarities
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TBLASTX
– TBLASTX
– The query is a nucleotide sequence
– The database is a nucleotide database
– All six frames are translated on the query and on the
database
– Coding :: Coding homology
– Searching distantly-related species
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– Sensitive but expensive
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BLAST output
1. List of sequences with scores
– Raw score
– Higher is better
– Depends on aligned length
– Expect Value (E-value)
– Smaller is better
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– Independent of length and database size
2. List of alignments
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Multiple Sequence Alignment
– Multiple Sequence Alignment (MSA) can be seen as a generalization of
a Pairwise Sequence Alignment (PSA). Instead of aligning just two
sequences, three or more sequences are aligned simultaneously.
– MSA is used for:
– Detection of conserved domains in a group of genes or proteins
(conservation analysis)
– Construction of a phylogenetic tree
– Prediction of a protein function/structure
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– Determination of a consensus sequence
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https://www.ebi.ac.uk/Tools/msa/
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https://www.ebi.ac.uk/Tools/<tool category> 41
Multiple Sequence Alignment Tools
https://www.ebi.ac.uk/Tools/msa/
– Clustal Omega
– Kalign
– MAFFT
– MUSCLE
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– T-Coffee
– EMBOSS Cons
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Multiple Sequence Alignment Tools
– Use heuristics
– Progressive alignment
– E.g. Clustal Omega
– Iterative alignment
– E.g. MAFFT, MUSCLE, Clustal Omega
– Consistency-based alignment
– E.g. T-Coffee
– Profile (HMM-based) alignment
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– E.g. Clustal Omega
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https://www.ebi.ac.uk/Tools/msa/clustalo
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Consensus Symbols
– An * (asterisk) indicates positions which have a single, fully conserved
residue.
– A : (colon) indicates conservation between groups of amino acids
with strongly similar properties
– A . (period) indicates conservation between groups of amino acids
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with weakly similar properties
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Things to remember
– Check the input size limit (depends on tool)
– Tool Errors (not a proper file format, if you provide a single sequence)
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Things to remember
– Input format
– Try using FASTA format
– Unique sequence identifiers
– First 30 characters in identifier should be unique
– Include sequence!
– Job can’t be found/other error
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– Results deleted after 7 days
– Some sequence/program combinations run out of memory
– Use a different program
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Which tool should I use?
– 3-100 sequences of typical protein length
– MUSCLE, T-Coffee, MAFFT, Clustal Omega
– 100-500 sequences
– Clustal Omega, MUSCLE, MAFFT
– >500 sequences
– Clustal Omega, Kalign
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Which tool should I use?
– Small number of unusually long sequence
– KALIGN, MAFFT (fast)
– DNA
– MAFFT, Kalign, MUSCLE
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Final remarks
– Don’t assume a single tool will cater for all your needs
– Change the parameters of the tools
– Remember where the tool excels and what its limitations are
– A tool intended for specific task A can also be used for task B (and
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may be better than the tool intended for task B specifically!)
– Crazy input will always give crazy results!
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