Plants have a family of photoreceptors known as phytochromes (phys). The model p
ID: 81069 • Letter: P
Question
Plants have a family of photoreceptors known as phytochromes (phys). The model plant Arabidopsis thaliana (A.t.) has five phytochrome genes, phyA - phyE. Your colleague has just cloned a phytochrome (Brapa_phy1) from Brassica rapa (B.r.) and wants to use Water to align their one B.r. phytochrome against all the Arabidopsis phy sequences. They use the command below. Does the command produce the results that they intended? If not, explain what went wrong and provide corrected code._
linux command line:
water At_phytochromes.fa BrapaPhytochrome.fa -gapopen 10 -gapextend 0.5 -outfile At_vs_Br.water
Explanation / Answer
The linux command line:
"water At_phytochromes.fa BrapaPhytochrome.fa -gapopen 10 -gapextend 0.5 -outfile At_vs_Br.water"
will not produce the corrected results.
There are some mandatory fields that need to be specified in the command line and the corrected command line is as follows:
water -bsequence At_phytochromes.fa -asequence BrapaPhytochrome.fa -gapopen 10 -gapextend 0.5 -outfile At_vs_Br.water
It is essential to add qualifier to mention reference file (using -bsequence option) and sequence file (using -asequence).