BLASTn maps DNA against DNA, for example gene sequences against a reference genome
blastn -query genes.ffn -subject genome.fna -outfmt 6 BLASTn tabular output format 6Column headers:qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore
Define your own output formatby adding the option -outfmt, as for example:
-outfmt "6 qseqid sseqid pident qlen length mismatch gapope evalue bitscore" supported format specifiers are: qseqid Query Seq-idqgi Query GIqacc Query accesionqaccver Query accesion.versionqlen Query sequence lengthsseqid Subject Seq-idsallseqid All subject Seq-id(s), separated by a ';'sgi Subject GIsallgi All subject GIssacc Subject accessionsaccver Subject accession.versionsallacc All subject accessionsslen Subject sequence lengthqstart Start of alignment in queryqend End of alignment in querysstart Start of alignment in subjectsend End of alignment in subjectqseq Aligned part of query sequencesseq Aligned part of subject sequenceevalue Expect valuebitscore Bit scorescore Raw scorelength Alignment lengthpident Percentage of identical matchesnident Number of identical matchesmismatch Number of mismatchespositive Number of positive-scoring matchesgapopen Number of gap openingsgaps Total number of gapsppos Percentage of positive-scoring matchesframes Query and subject frames separated by a '/'qframe Query framesframe Subject framebtop Blast traceback operations (BTOP)staxids Subject Taxonomy ID(s), separated by a ';'sscinames Subject Scientific Name(s), separated by a ';'scomnames Subject Common Name(s), separated by a ';'sblastnames Subject Blast Name(s), separated by a ';' (in alphabetical order)sskingdoms Subject Super Kingdom(s), separated by a ';' (in alphabetical order) stitle Subject Titlesalltitles All Subject Title(s), separated by a '<>'sstrand Subject Strandqcovs Query Coverage Per Subjectqcovhsp Query Coverage Per HSPdefault values are:
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