There are two ways of using BLAST

• Going to NCBI’s website: https://blast.ncbi.nlm.nih.gov/
  • Runs in NCBI servers with NCBI databases
• Using a command line version
  • Runs in our server with our databases
  • can also send jobs in NCBI servers with NCBI databases
  • Download it from NCBI website

For today we can look at NCBI page

megablast

Highly similar sequences

discontiguous megablast

More dissimilar sequences

blastn

Somewhat similar sequences

blastp

protein-protein BLAST.

PSI-BLAST

Position-Specific Iterated BLAST.

builds a position-specific scoring matrix.

PHI-BLAST

Pattern Hit Initiated BLAST.

limits alignments to those that match a pattern in the query.

Quick BLASTP

Accelerated protein-protein BLAST.

very fast and works best if the target percent identity is 50% or more.

DELTA-BLAST

Domain Enhanced Lookup Time Accelerated BLAST.

builds a PSSM using a Conserved Domain Database search.

searches a sequence database.

• Write a document explaining the details of BLAST algorithms
• Each student takes a different algorithm
  • megablast and discontiguous megablast
  • PSI-BLAST
  • PHI-BLAST
  • Quick BLASTP
  • DELTA-BLAST
  • and …

Explain what are these options

• Low complexity regions filter
• Mask for lookup table only
• Mask lower case letters

Understand and explain

• why the algorithm is useful
• how does it work
• what is the difference with the standard BLAST
• Read the associated paper

Use your words: Do not copy and paste

Give proper references when citing someone else’s work

nr

Non-redundant protein sequences

refseq_protein

Reference proteins

landmark

Model Organisms

swissprot

UniProtKB/Swiss-Prot

pat

Patented protein sequences

pdb

Protein Data Bank proteins

env_nr

Metagenomic proteins

tsa_nr

Transcriptome Shotgun Assembly proteins

Human G+T

Human genomic plus transcript

Mouse G+T

Mouse genomic plus transcript

nr/nt

Nucleotide collection

Bacteria and Archaea

16S ribosomal RNA sequences

refseq_rna

Reference RNA sequences

refseq_representative_genomes

RefSeq Representative genomes

refseq_genomes

RefSeq Genome Database

wgs

Whole-genome shotgun contigs

est

Expressed sequence tags

SRA

Sequence Read Archive

TSA

Transcriptome Shotgun Assembly

HTGS

High throughput genomic sequences

pat

Patent sequences

pdb

Protein Data Bank

refseq_genomic

Reference genomic sequences

RefSeq_Gene

Human RefSeqGene sequences

gss

Genomic survey sequences

dbsts

Sequence tagged sites

Let’s look for Teje’s data

This is a 16S gene amplified by PCR

There is no “official” taxonomy. People are still figuring out many cases

NCBI has an “unofficial” taxonomy tree

Trees have root, branches, internal nodes and leaves

Edges (branches) connect nodes

Each node (except the root) has one unique parent node

A node can have several descendants. If a node has no descendants, we call it a leave

Each node has

• a unique id called taxid
• An official scientific name (as Linnaeus designed)
• Any alternative alias by which the organism can be known
• The taxid of the parent
• zero or more descendants

Using NCBI taxid prevents many errors