Go Back   SEQanswers > Sequencing Technologies/Companies > Pacific Biosciences

Similar Threads
Thread Thread Starter Forum Replies Last Post
Combine FASTA files in a specific order based on sequence ID N311V Bioinformatics 9 09-08-2014 11:19 AM
Basic data extraction on bam files Philcolson Bioinformatics 5 09-24-2013 05:20 AM
piRNAs sequence files in fasta format for rat and mapping small RNA seq reads TJC Epigenetics 0 10-08-2012 02:11 PM
search fasta maria_mari Bioinformatics 2 06-11-2012 03:28 AM
quick basic questions about files cutcopy11 Bioinformatics 0 04-20-2012 02:01 PM

Thread Tools
Old 09-16-2013, 06:18 AM   #1
Junior Member
Location: Philadelphia, PA

Join Date: Jul 2013
Posts: 4
Question Very basic search for sequence fragments within CCS fasta files

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,
hammers13 is offline   Reply With Quote
Old 09-18-2013, 10:09 AM   #2
Junior Member
Location: Philadelphia, PA

Join Date: Jul 2013
Posts: 4

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...
hammers13 is offline   Reply With Quote
Old 11-19-2014, 09:08 AM   #3
Brian Bushnell
Super Moderator
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

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?
Brian Bushnell is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 07:12 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO