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How does one Stockholm

I have created an annotated genome assembly. I have the final assembly in genbank form and a selection of fasta files, as well as the raw reads (both illumina and nanopore). I also have various intermediate files such as .bam and .paf and

I have been looking and googling and searching and running programs and scripts for days. Nothings seems to be able to create stockholm files. Can somebody please explain how I create a stockholm file that is viable for input into programs that screen for non-coding RNA (CMsearch).

I just can't find anywhere that explains how to create a stockholm file. Can anybody help me?

rna alignment genome stockholm
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updated by Mensur Dlakic Mensur Dlakic • written by bakajack • bakajack

1 answer

There is a utility program called esl-reformat inside of the HMMer package. It can convert between all major alignment formats, including Stockholm. Major protein and RNA databases such as Pfam and Rfam use this format, and there are file examples on their webpages if go for family alignments. reformat.pl script from the HH-suite package can convert to Stockholm as well.

You may also want to look through the Infernal package. Most programs that deal with RNA alignments should be able to write them out in Stockholm format.

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written by Mensur Dlakic Mensur Dlakic

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