Atul's Research

Pandoc - Document Converter Came across this tool on Ubuntu - Pandoc - Universal Document Converter. Very handy tool to convert between different formats. I had to convert a LibreOffice Writer document to EPUB format. pandoc test.odt -f odt -t epub -s -o test.epub test.odt - original document in odt format -f - input format -t - output format -s - standalone document -o - output file

Using the standalone NCBI BLAST I am describing the use of a standalone BLAST () on a Ubuntu 22.04.4 LTS system. You can get a lot of details at the NCBI BLAST Manual site . I will stick to the components i require for my work. Building a BLAST database from local sequences The makeblastdb application produces BLAST databases from FASTA files.  Use the –parse_seqids flag when invoking makeblastdb to enable retrieval of sequences based upon sequence identifiers. It is  possible to fetch individual sequences using blastdbcmd or to limit the search with the –seqidlist option.  In this case, each sequence must have a unique identifier, and that identifier must have a specific format. The identifier should begin right after the “>” sign on the definition line, contain no spaces. specify its type ( -dbtype nucl/prot) name the output database with the same base name ( -out hs_chr) overwriting the existing one. -title for name of the Database makeblastdb -in ...