BIOINFORMATICS
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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. BWA (BURROWS-WHEELER ALIGNER)
2.1. BWA-backtrack (Short reads)
2.1.1. Backtracking
2.1.2. Up to 100bp
2.2. BWA-SW (Longer reads)
2.2.1. Smith-Waterman
2.2.2. 70bp to megabases
2.3. BWA-MEM (Low-divergent)
2.3.1. MEM seeding
2.3.2. Smith-Waterman extension
2.3.3. Supports chimeric alignments
3. BOWTIE
3.1. Ultrafast
3.1.1. Greedy search
3.1.2. Quality-aware
3.1.3. Burrows-Wheeler index
3.2. Aligns short reads
3.2.1. 35bp reads
3.2.2. Large genomes