DNA

Two routines have been written to scan DNA base sequences and return locations on chromosome 1 of the T2T genome spec ( T2Tchm13.draft_v1.1.fasta.gz ). The software runs on Windows 7 and higher. Two zip files Symsyn DNA code.zip and T2T Chromosome 1 bp files.zip are downloaded to a folder named \T2T ( for example), and unzipped in place. The routines are run from the command line. Change the default folder to \T2T.


Findbp locates a specified base sequence in the chromosome and returns the locations.

sss findbp t2tchr1 seq.txt result.txt

sss findbp t2tchr1 'AAACCTTGGGGTAGATAG result.txt


sss is the run time interpreter

t2tchr1 is the name of the chromosome file

seq.txt is the text file containing the search sequence

AAACCTTGGGGTAGATAG is a literal string (preceded by a single quote) instead of seq.txt

result.txt (optional) is the name of the created text file containing the results of the query


Showbp returns the base sequence at the specified location.

sss showbp t2tchr1 123456 99 result.txt

123456 is the starting location

99 is the character count


Comments

Isaac @ qsys.us