How to use HMMER to find a gene sequence within in a full genome sequence file. Video #3.

In this video we are using HMMER to look for the translation elongation factor (TEF) 1 alpha gene within a full genome assembly file.
Commands used within this video:
(NOTE THAT ANGLED BRACKETS ARE NOT ALLOWED IN THE DESCRITPTION SO I HAVE REPLACED THEM WITH "ANGLED BRACKET")
#Make a MSA:
/nfs1/BPP/LeBoldus_Lab/user_folders/mcmurtrs/bin/bin/mafft TEF1_copy.fasta ANGLED BRACKET TEF1_aligned.msa
hmmbuild TEF1_ref.hmm TEF1_aligned.msa
cp /nfs4/BPP/Anderson_LeBoldus/LeBoldus/mcmurtrs/De_novo/A-2_Ass/A-2.spades.fasta .
#Throws an error for large sequences (i.e. full genome sequences)
hmmsearch TEF1_ref.hmm A-2.spades.fasta
Searches very large sequence files:
nhmmer TEF1_ref.hmm A-2.spades.fasta
nhmmer -A A-2.hits.txt TEF1_ref.hmm A-2.spades.fasta
esl-reformat fasta A-2.hits.txt ANGLED BRACKET A-2.hits.fasta
Putting it together:
nhmmer -A A-2.hits.txt TEF1_ref.hmm A-2.spades.fasta | esl-reformat fasta A-2.hits.txt ANGLED BRACKET A-2.hits.fasta

[@mariapayro2523]

Thank you very much. It was really useful. Greetings from Mexico!