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Old 09-16-2013, 06:18 AM   #1
hammers13
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Location: Philadelphia, PA

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Question Very basic search for sequence fragments within CCS fasta files

Hello,
I am trying to figure out the best way to find defined sequences within the 6 fasta-files from CCS sequencing with 2 cells on PacBio RSII.

What I would like to do is find exact (and similar matches!) of a given sequence (50-60 bp) within all sequences I got from sequencing. Importantly, I want to do the search in two directions (5'-3'; 3'-5').

I tried to read and understand the BLAST+ manual, but I am not into informatics and wonder whether there is a more convenient way (with a graphic user interface?) for me to do so... I am using MacOS X 10.7.5.

Your help would be greatly appreciated.
Thank you very much,
Chris
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Old 09-18-2013, 10:09 AM   #2
hammers13
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I now got blast+ to work and use tblastx for my purposes. Actually it wasn't that difficult, I was just somewhat deterred by the "non-graphical" terminal-input...
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Old 11-19-2014, 09:08 AM   #3
Brian Bushnell
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Quote:
Originally Posted by kurban910 View Post
Hello, i am trying to find out the best way to find same or similar sequences to the defined sequence within the transcriptome sequences in fasta file, which is assembled from RNA-seq data. i know there r many tools, but i dont know which one is developed for this purpose. could any one give me some tips?
thanks?
Cross-posted: https://www.biostars.org/p/120417/
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