Looking for a method to filter out data from related BLAST results

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• 
  Vladimir Vladimirov · Virginia Commonwealth University

  I'm not sure if that's gonna help but you can try ASAP, just google it, it should come on the first page, it's free software for excel, has lots of features, you may try it and see if it helps. On other note i might not have understood what you want to do. Do you want to identify ncRNA sequences among all ESTs? If so, why don't you just filter everything against the mirbase? you should be able to detect all ncRNAs, assuming that's what you looking for.

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  I'm not sure if that's gonna help but you can try ASAP, just google it, it should come on the first page, it's free software for excel, has lots of features, you may try it and see if it helps. On other note i might not have understood what you want to do. Do you want to identify ncRNA sequences among all ESTs? If so, why don't you just filter everything against the mirbase? you should be able to detect all ncRNAs, assuming that's what you looking for.

  Jun 20, 2012
• 
  Ajay Saini · Bhabha Atomic Research Centre

  Hi Yevgeniy I have done a similar problem few years ago...where I could use excel to arrange the blast results, sort the results based on the blast out put values and filter the non-essentail entries....I actually down loaded the databases for coding sequencing, non-coding sequences and made individual local databases on my PC...and I was performing local blast searches on these databases.....everything I was doing on Excel was on my own and not anyother software or tool.....the best thing was I was able to do filtering of sequences after doing the blast...but the steps were very slow and ....these searches and analysis on excel (if the files are huge) takes a lot of time....I hope better tools will be available now... bye

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  Hi Yevgeniy
  
  I have done a similar problem few years ago...where I could use excel to arrange the blast results, sort the results based on the blast out put values and filter the non-essentail entries....I actually down loaded the databases for coding sequencing, non-coding sequences and made individual local databases on my PC...and I was performing local blast searches on these databases.....everything I was doing on Excel was on my own and not anyother software or tool.....the best thing was I was able to do filtering of sequences after doing the blast...but the steps were very slow and ....these searches and analysis on excel (if the files are huge) takes a lot of time....I hope better tools will be available now...
  bye

  Jun 20, 2012
• 
  Saurabh Gayali · National Institute of Plant Genome Research

  Can u send a sample data with telling where is the info of descimination. I will tell u the formula to do it in excel

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  Can u send a sample data with telling where is the info of descimination. I will tell u the formula to do it in excel

  Jun 20, 2012
• 
  Richard Jones · Technical Analyst

  Send a sample? Unix utilities "Sed, Ed, Awk, Nawk, and Grep", or Excel or WinGrep

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  Send a sample? Unix utilities "Sed, Ed, Awk, Nawk, and Grep", or Excel or WinGrep

  Jun 20, 2012
• 
  Yevgeniy Kharonov · City University of New York - Bernard M. Baruch College

  Hey all, Thank you for your answers. However, I have found a very simple solution. Using Galaxy (https://main.g2.bx.psu.edu/) tools I can convert the columns of interest using Convert delimiters to TAB, to remove white spaces and then using Join, Subtract, Group -Compare two Datasets tool to find common or distinct rows to display only non-matching alignments.

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  Hey all,
  
  Thank you for your answers. However, I have found a very simple solution. Using Galaxy (https://main.g2.bx.psu.edu/) tools I can convert the columns of interest using Convert delimiters to TAB, to remove white spaces and then using Join, Subtract, Group -Compare two Datasets tool to find common or distinct rows to display only non-matching alignments.

  Jun 20, 2012
• 
  Yevgeniy Kharonov · City University of New York - Bernard M. Baruch College

  I have heard of blast2go and how it is useful for annotations which I my include in my workflow a bit later on. Just to update there is another method using excel LOOKUP formula For example Copying the query id column from blastx with %identity>85 into the blastn results column AA, you can create a new column , B and use =lookup(A2,$AA$1:$AA$50,000). Then copy the formula into all B rows adjacent to an A row , until the last A row. Hope that made sense. Once the formula finishes you copy A and B and paste as values into AB/AC to enable further data sorting. This formula yielded better results than the galaxy compare tool because it is still in excel, no need to use .txt delimited...

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  I have heard of blast2go and how it is useful for annotations which I my include in my workflow a bit later on. Just to update there is another method using excel LOOKUP formula
  
  For example
  Copying the query id column from blastx with %identity>85 into the blastn results column AA, you can create a new column , B and use =lookup(A2,$AA$1:$AA$50,000). Then copy the formula into all B rows adjacent to an A row , until the last A row. Hope that made sense. Once the formula finishes you copy A and B and paste as values into AB/AC to enable further data sorting.
  
  This formula yielded better results than the galaxy compare tool because it is still in excel, no need to use .txt delimited...

  Jun 20, 2012
• 
  Saurabh Gayali · National Institute of Plant Genome Research

  Vlookup in excel is best, specially when i found to search non unique datasets too :)

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  Vlookup in excel is best, specially when i found to search non unique datasets too :)

  Jun 21, 2012
• 
  Antonio Sanz · Universidad de Valladolid

  Probably this article will help you. Http://bib.oxfordjournals.org/content/8/1/6.full.pdf+html

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  Probably this article will help you.
  Http://bib.oxfordjournals.org/content/8/1/6.full.pdf+html

  Jul 3, 2012