BLASTn maps DNA against DNA, for example: mapping a gene sequences against a reference genome
blastn -query genes.fasta -subject genome.fasta -outfmt 6
Column headers:
qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore
1. qseqid query or source (gene) sequence id
2. sseqid subject or target (reference genome) sequence id
3. pident percentage of identical positions
4. length alignment length (sequence overlap)
5. mismatch number of mismatches
6. gapopen number of gap openings
7. qstart start of alignment in query
8. qend end of alignment in query
9. sstart start of alignment in subject
10. send end of alignment in subject
11. evalue expect value
12. bitscore bit score
by adding the option -outfmt, as for example:
-outfmt "6 qseqid sseqid evalue"
supported format specifiers are:
qseqid Query Seq-id
qgi Query GI
qacc Query accesion
qaccver Query accesion.version
qlen Query sequence length
sseqid Subject Seq-id
sallseqid All subject Seq-id(s), separated by a ';'
sgi Subject GI
sallgi All subject GIs
sacc Subject accession
saccver Subject accession.version
sallacc All subject accessions
slen Subject sequence length
qstart Start of alignment in query
qend End of alignment in query
sstart Start of alignment in subject
send End of alignment in subject
qseq Aligned part of query sequence
sseq Aligned part of subject sequence
evalue Expect value
bitscore Bit score
score Raw score
length Alignment length
pident Percentage of identical matches
nident Number of identical matches
mismatch Number of mismatches
positive Number of positive-scoring matches
gapopen Number of gap openings
gaps Total number of gaps
ppos Percentage of positive-scoring matches
frames Query and subject frames separated by a '/'
qframe Query frame
sframe Subject frame
btop 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 Title
salltitles All Subject Title(s), separated by a '<>'
sstrand Subject Strand
qcovs Query Coverage Per Subject
qcovhsp Query Coverage Per HSP
default values are:
-outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore"
blastn -help