BIOINFORMATICS

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BIOINFORMATICS by Mind Map: BIOINFORMATICS

1. BLAST (BASIC LOCAL ALIGNMENT SEARCH TOOL)

1.1. FUNCTION

1.1.1. ALLOWS THE USER TO SELECT ONE SEQUENCE (QUERY) AND PERFORM PAIRWISE ALIGNMENT BETWEEN QUERY AND TARGET

1.2. SEARCH STEPS

1.2.1. 1) SPECIFYING SEQUENCE OF INTEREST

1.2.1.1. ACCESSION NUMBER

1.2.1.2. CUTTING OR PASTING DNA OR PROTEIN IN FASTA

1.2.2. 2) SELECTING BLAST PROGRAMMES

1.2.2.1. Blastp

1.2.2.2. Blastn

1.2.2.3. Blastx

1.2.2.4. tBlastn

1.2.2.5. tBlastx

1.2.3. 3) SELECTING DATABASE

1.2.3.1. PROTEIN SEQUENCE DATABASE

1.2.3.2. NUCLEOTIDE SEQUENCE DATABASE

1.2.4. 4a) SELECTING OPTIONAL SEARCH PARAMETERS

1.2.5. 4b) SELECTING FORMATTING PARAMETERS

2. PAIRWISE SEQUENCE ALIGNMENT

2.1. SCORING MATRIX

2.1.1. PAM

2.1.2. BLOSUM

2.2. ALIGNMENT ALGORITHM

2.2.1. GLOBAL ALIGNMENT

2.2.1.1. 1) SETTING UP MATRIX

2.2.1.2. 2) SCORING THE MATRIX

2.2.1.3. 3) IDENTIFY THE OPTIMAL ALIGNMENT

2.2.2. LOCAL ALIGNMENT

2.3. TERMS

2.3.1. HOMOLOGY

2.3.2. SIMILARITY

2.3.3. IDENTITY

2.3.4. ORTHOLOGS

2.3.5. PARALOGS

2.3.6. GAPS

2.3.7. REFSEQ