Entering edit mode
5.1 years ago
shashankch9009 • 0
When converting the fasta file to its equivalent BWT (Burrow wheeler transform), why ais the BWT file in as shown below (not containing ATGC but some symbols), I do see the BWT file size as lesser than the fasta file (indicating compression)
g üÿóýW?ýÿÿ÷ßßýÿÿ?ßÿÿÿþ_ÿÿÏÿõò_Ž €/H žPH pg ÿÿïßÿÿÿÿuÿùßÿó?ÿÿÿÿÿóÿýo÷÷ýÿýÿÿõ_Ž /H ¡PH Ýg ÿÿüÿÿüý¿ßÿÿ?ÿÿÿþÿÿÿÿÿÿïÿÿóÿÿ÷ÿù_Ž ’/H ¤PH Qh ÿ÷ÿ÷ÿÿÿüÿÿ÷ÿÿýÿÿÿÿ÷ÿÿÿÿÿßÿÿÿÿÿÿú_Ž ™/H ¤PH Éh ÿÿÿÿsÿ÷ÿßÿ÷ÿß}ßÿÿÿ÷ÿ?ÿ×ÿÿÿÿÿÿÿÿÿü_Ž ¤/H ¤PH <i ÿÿÿÿÿ}ÿÿ?ÿ?ÿÿÿÿÿÿÿÿÿûÿÿÿÿ÷ÿïÿ_ÿþ_Ž ª/H ¦PH ²i ÷÷ÿÿÿÿÿÿÿÿÿÿüï÷ÿÿÿûÿÿ}ÿÿÿß=ÿïÿÿ `Ž ²/H ©PH %j ßßÿÿÿßÿÿýÿÿÿßÿÿýýÿßÿ÷ÿýÿÿÿóÿßÿ`Ž ¿/H ©PH —j ûÿÿ\õÿÿüÿÿ?ÿwÿÿÿÿÿÿÿÿÿýÿÿ?ßßÿ`Ž Ë/H ªPH k óÿÿOÿÿÿÿÿýÿÿßÿ÷ýßñûÿÿÿÿ÷ÿqÿÿ `Ž Ù/H «PH sk ýÿÿÿ×ÿÿÞÿ÷ÿóÿý÷÷üÿÏÿÿÿÿÿ÷ÿ÷ÿÏÿ
What tool have you used for computing the BWT? Note that the BWT itself does not reduce the size of the input string. For that run length encoding, move to front, lz or something similar is required.
shashankch9009 : You need to provide additinal information about what you are trying to do and what program (your own or external) you are using. There isn't a logical question in the post as currently written.
WikiPedia has a page that explains BWT. There are online tools that demonstrate the transform. Here is one.