linyunliu / bioinformatics

Unraveling Evolutionary Relationship between Fungi Species

ABOUT

Contribution

Linyun Liu, Tarandeep Kaur, Shika Borge

Research Question

How can analyzing protein sequences between Saccharomyces Cerevisiae, Schizosaccharomyces Pombe and other fungi species reveals the evolutionary relationships?

Objective

To construct phylogenetic tree from protein clusters using maximum likelihood method to reveal evolutionary relationship between Saccharomyces Cerevisiae, Schizosaccharomyces Pombe and other Fungi species

CONNECT FTP TO DOWNLOAD COMMAND LINE TOOL

ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

REFERENCES

1. Blast Software General Introduction

2. How to blast against a particular set of local sequences (local database)?

3. Building a BLAST database with your (local) sequences

4. Blast Command Line Tool User Mannual:

ALIGNMENT FILE OUTPUT OPTIONS (-outfmt x)

x	Description
0	pairwise
1	query-anchored showing identities
2	query-anchored no identities
3	flat query-anchored, show identities
4	flat query-anchored, no identities
5	XML Blast output
6	tabular
7	tabular with comment lines
8	Text ASN.1
9	Binary ASN.1
10	Comma-separated values
11	BLAST archive format (ASN.1)
12	Seqalign (JSON)
13	Multiple-file BLAST JSON
14	Multiple-file BLAST XML2
15	Single-file BLAST JSON
16	Single-file BLAST XML2
17	Sequence Alignment/Map (SAM)
18	Organism Report

COMMAND LINE USAGE

1. Making BLAST database of local sequences

The input file must consist of sequences in FASTA format.

$ makeblastdb -in sequence.fasta -parse_seqids -dbtype prot -out /PATH/TO/YOUR/DTATABASE

Here, -parse_seqids is used because it may later help in parsing the sequence ids of the given sequences for further analyses. -in refers to the input file, -dbtype can be protein or nucleotide and -out is the name of the BLAST database to be created. If your input file is present in another directory then provide the complete path.

2. BLAST the local database against a single sequence

$ blastp -db /PATH/TO/YOUR/DTATABASE -query seq.fasta -outfmt 0 -out result.txt
$ blastp -db /PATH/TO/YOUR/DTATABASE -query seq.fasta -outfmt 5 -out result.xml

where, -db is the BLAST database created in the previous step, -query is a file consisting of FASTA sequence, -outfmt is the output format which can be defined in several ways as shown here, and -numthreads refers to the number of CPUs to be used during the search. In the case of nucleotide sequences, use blastn or any other appropriate blast executable.

3. All against all

To BLAST local sequences against the local database created from the same input sequences, the input sequences are used as a query file in FASTA format.

$ blastp -db blastdb -query sequence.fasta -outfmt 0 -out result.txt

As you can see in the above command, the database is the same local database created in the first step and the query are the input sequences from which the local database was created in the first place.