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This article mainly introduces "how to use Blast comparison software". In daily operation, I believe many people have doubts about how to use Blast comparison software. The editor consulted all kinds of materials and sorted out simple and easy-to-use operation methods. I hope it will be helpful to answer the doubts about "how to use Blast comparison software". Next, please follow the editor to study!

Blast alignment software is probably the most commonly used short sequence local alignment software, but it has many parameters, some of which have not been studied carefully, as follows: # add blast alignment result information

The-outfmt parameter of blast so that blastp-help can view the information for each output format, as follows:

* Formatting options-outfmt alignment view options: 0 = Pairwise, 1 = Query-anchored showing identities, 2 = Query-anchored no identities, 3 = Flat query-anchored showing identities, 4 = Flat query-anchored no identities, 5 = BLAST XML, 6 = Tabular, 7 = Tabular with comment lines, 8 = Seqalign (Text ASN.1), 9 = Seqalign (Binary ASN.1), 10 = Comma-separated values, 11 = BLAST archive (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, 18 = Organism Report Options 6, 7 and 10 can be additionally configured to produce a custom format specified by space delimited format specifiers. The supported format specifiers are: qseqid means Query Seq-id qgi means Query GI qacc means Query accesion qaccver means Query accesion.version qlen means Query sequence length sseqid means Subject Seq-id sallseqid means All subject Seq-id (s), separated by a' 'sgi means Subject GI sallgi means All subject GIs sacc means Subject accession saccver means Subject accession.version sallacc means All subject accessions slen means Subject sequence length qstart means Start of alignment in query qend means End of alignment in query sstart means Start of alignment in subject send means End of alignment in subject qseq means Aligned part of query sequence sseq means Aligned part of subject sequence evalue Means Expect value bitscore means Bit score score means Raw score length means Alignment length pident means Percentage of identical matches nident means Number of identical matches mismatch means Number of mismatches positive means Number of positive-scoring matches gapopen means Number of gap openings gaps means Total number of gaps ppos means Percentage of positive-scoring matches frames means Query and subject frames separated by a'/ 'qframe means Query frame sframe means Subject frame Btop means Blast traceback operations (BTOP) staxid means Subject Taxonomy ID ssciname means Subject Scientific Name scomname means Subject Common Name sblastname means Subject Blast Name sskingdom means Subject Super Kingdom staxids means unique Subject Taxonomy ID (s) Separated by a' '(in numerical order) sscinames means unique Subject Scientific Name (s), separated by a'; 'scomnames means unique Subject Common Name (s), separated by a'; 'sblastnames means unique Subject Blast Name (s), separated by a';'(in alphabetical order) sskingdoms means unique Subject Super Kingdom (s), separated by a' '(in alphabetical order) stitle means Subject Title salltitles means All Subject Title (s), separated by a' 'sstrand means Subject Strand qcovs means Query Coverage Per Subject qcovhsp means Query Coverage Per HSP qcovus means Query Coverage Per Unique Subject (blastn only)

In fact, we generally use-outfmt 5 or-outfmt 6, the former output XML format, the latter output TAB segmentation format; the former is more informative and useful, while the latter is the most commonly used format (which some software likes to call)

The information for each column in TAB format is as follows (you can understand it with the instructions above):

Qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore

But sometimes we want more than the above 12 columns of information. For example, I also want to know the coverage information of the comparison results (qcovs:Query Coverage Per Subject).

In fact, you only need to add the column ID that needs to be added in advance in the blast comparison command, such as adding coverage information on the basis of outfmt 6:

-outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovs"

Note: if you need several columns, you can add it all the way up, space division

At this point, the study on "how to use the Blast comparison software" is over. I hope to be able to solve your doubts. The collocation of theory and practice can better help you learn, go and try it! If you want to continue to learn more related knowledge, please continue to follow the website, the editor will continue to work hard to bring you more practical articles!

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