Comparison tools and tools

Comparison tools and tools

(Green) short pairwise alignment/detailed edit model; (yellow) database search/divergent homology detection; (red) whole genome alignment/alignment of long sequences with structural rearrangements; (blue) short read mapping/rapid alignment of massive numbers of short sequences.

Simple local comparison: Blast, Blat, etc.

Blast types include: blastn --- comparison of the nucleic acid sequence in the database and the nucleic acid sequence in the database-comparison of the protein sequence in the database-Blastx --- translation of the nucleic acid sequence into a protein (six-frame protein) then compare with the protein sequence in the database Tblastn --- compare the protein sequence with the nucleic acid sequence in the database Tblastx --- compare with the protein sequence translated from the database after the nucleic acid sequence is translated into a protein sequence. BLAST the process of creating a database is to create an index file of the target sequence, the program used is formatdb. Generally, we use the FASTA format sequence as the input. The FASTA sequence used for database creation is db. seq. The basic commands for formatdb are:

Formatdb-I db. seq [-options]

Common parameters include:

-P: select the database type. T indicates the protein library, and F indicates the nucleic acid library. The default value is T.
-O: Determine whether to analyze the sequence name and create a sequence name index. T indicates that a sequence name index is created, and F indicates that no sequence name index is created. The default value is F.
BLAST command line:

Output result:

3 is similarity, 4 is the area that can be compared

Blat

Global Comparison: MUSCLE, MATT, etc.

Muscle-in <inputfile>-out <outputfile>