Remote Blast
Somewhat amazingly I didn’t realize how easy/awesome blast’s -remote flag is. Heres a piece of the human beta globin gene blasted against NCBI’s nt db. This is an immensely useful feature; thank you NCBI.
#make a small fastafile
echo -e ">hemoglobinbeta\nTGTGTGCTTATTTGCATATTCATAATCTCCCTACTTTATTTTCTTTTATTTTT\n" > testseq.fna
#blast outfmt 6 is tabular
blastn -db nt -query testseq.fna -remote -outfmt 6
hemoglobinbeta gi|1036032571|gb|AH001475.2| 100.00 57 0 0 1 57 2405 2461 3e-20 106
hemoglobinbeta gi|970597825|gb|KU350152.1| 100.00 57 0 0 1 57 1269 1325 3e-20 106
hemoglobinbeta gi|970597823|gb|KR028331.1| 100.00 57 0 0 1 57 1269 1325 3e-20 106
hemoglobinbeta gi|730321889|gb|KM504957.1| 100.00 57 0 0 1 57 843 899 3e-20 106
hemoglobinbeta gi|302313136|gb|GU324922.1| 100.00 57 0 0 1 57 2844 2900 3e-20 106
hemoglobinbeta gi|288899267|gb|GU372416.1| 100.00 57 0 0 1 57 231 287 3e-20 106
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#the default format includes alignments
blastn -db nt -query testseq.fna -remote
>gb|AH001475.2| Homo sapiens beta-globin gene, complete cds
Length=4355
Score = 99.0 bits (53), Expect = 4e-18
Identities = 53/53 (100%), Gaps = 0/53 (0%)
Strand=Plus/Plus
Query 1 TGTGTGCTTATTTGCATATTCATAATCTCCCTACTTTATTTTCTTTTATTTTT 53
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Sbjct 2405 TGTGTGCTTATTTGCATATTCATAATCTCCCTACTTTATTTTCTTTTATTTTT 2457
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