nucleotide Hidden Markov Model search
I am using HMMER v3.1 for nucleotide Hidden Markov Model searches.
What I can't find in the manual is whether the hmm (I am building species-specific domain specific hmm) used to search a database looks at the plus and minus strand of the sequences in the database. To clarify - when running a BLAST the output gives matches against both forward and reverse. I am not sure if this occurs with HMMER. Can anyone help with this?
• 2,335 views
•
link
updated
by
Biostar
•
written
by
peri.tobias •
•
written
by
peri.tobias •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
RNA seq strandedness (reverse-strand)
written by ZuelTech •
-
What is Bowtie2 --norc parameter?
written by lvl2111 •
-
How pfam is made?
written by GenesisBio •
-
What should I use as a reference in hivmmer
written by nadinezakkak •
-
Best way to identify proteins within a family?
written by Solowars
-
Genome Studio confusing SNP allele coding schema, what is the main genotype of the sample?
written by mittu1602
-
Does hmmsearch look at the reverse complement of the fasta?
written by uwe.menzel •
-
Megabast multistrand alignment
written by rangerunseen •
-
STAR BAM into RSEM
written by Biogeek
-
Program to extract sequences corresponding to the miRNA alignment with flanking sequences from both…
written by shaanbdu •
