Problem with extract aligment from a blast result to a fasta file....

Question

[sebastian.f.ing]

I have a metagenome like a db, and I need to blast a genome with this metagenome, the results are very wide, and I need to extract the alignment from this result and put into a fasta file, but I can't, because the result are in a *.html file. I do this:

formatdb

formatdb -i home/biolinux/Desktop/prueba/Metagenoma/l1l2/4499203.3.350.genecalling.coding.faa

Blastp

blastall \
  -p blastp \
  -d /home/biolinux/Desktop/prueba/Metagenoma/l1l2/4499203.3.350.genecalling.coding.faa \
  -T T \
  -i /home/biolinux/Desktop/prueba/Nitrincola.gbk \
  -o /home/biolinux/Desktop/prueba/resulnitri.html

Later I try to do a fastacmd, but I can't

What can I do?

Answer 1

[st.ph.n]

I would first recommend you update the BLAST cli you're using to the latest release. (ncbi-blast-2.2.29+)

The command to make the db would then be:

makeblastdb -in <input file> -input_type <file type> -dbtype <molecule type> -out <database name>

then for blastp:

blastp -db <database name> -query <input_file> -out <output file name> -outfmt <**format> -num_threads int_value (if you have more CPUs at your disposal

alignment view options:

0 = pairwise,
1 = query-anchored showing identities,
2 = query-anchored no identities,
3 = flat query-anchored, show identities,
4 = flat query-anchored, no identities,
5 = XML Blast output,
6 = tabular,
7 = tabular with comment lines,
8 = Text ASN.1,
9 = Binary ASN.1
10 = Comma-separated values
11 = BLAST archive format (ASN.1)

Choose the output format that best fits what you want to do. When I want to get a new fasta of results, I often will output in the tabular format, and using unix commands and python will sort the evalues in column 11, and toss out hits I don't want. I pull out the desired IDs from the first column, and then pull the corresponding sequences and headers from the original fasta file given the id's from the blast output.