[BiO BB] Search reverse repeat - Bayesian Filter detected spam

Tanney, Austin Austin.Tanney at arragen.com
Tue Jun 1 12:48:57 EDT 2004


Sorry thats completely correct... I read that quite quickly and thought it was a more simple question.

These are basically two identical sequences in different orientations. You could do as Martin says and compliment them but it does beg the question... why? Are you not ignoring the biological implications? Its one thing to turn the sequence back to front on a computer but that doesnt really have much biological significance. Unless your sequence is just in the wrong orientation. 

> -----Original Message-----
> From: Martin Gollery [mailto:mgollery at unr.edu]
> Sent: 01 June 2004 17:22
> To: bio_bulletin_board at bioinformatics.org
> Subject: Re: [BiO BB] Search reverse repeat - Bayesian Filter detected
> spam
> 
> 
> I don't believe the reverse complement idea will work, 
> because these two 
> sequences are reversed, but not complements. What you could 
> do is use a 
> script to complement them, then run Blast with reverse complement 
> switched on.
> 
> Tanney, Austin wrote:
> 
> > Run BLAST ensuring that you use the "reverse complement" 
> BLAST. I am pretty sure most versions of BLAST have this
> > If you are just interested in BLASTing two sequences 
> specifically against one another use this
> > http://www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html
> > 
> > Cheers
> > 
> > Austin
> > 
> > 
> >>-----Original Message-----
> >>From: Zhang, Yuanji [mailto:yjzhang at noble.org]
> >>Sent: 01 June 2004 16:47
> >>To: 'bio_bulletin_board at bioinformatics.org'
> >>Subject: [SPAM] - [BiO BB] Search reverse repeat - Bayesian Filter
> >>detected spam
> >>
> >>
> >>Which similarity search program will align reverse repeats in 
> >>the genome?
> >>For example, if I have 2 sequences, 
> >>
> >>>Seq A
> >>
> >>AATCATCAATCAGCCACTACCAAAAAATGCTCTCTGGAGTTGGTTTTCTTTTATTGATAC
> >>
> >>and 
> >>
> >>
> >>>Seq B
> >>
> >>CATAGTTATTTTCTTTTGGTTGAGGTCTCTCGTAAAAAACCATCACCGACTAACTACTAA
> >>
> >>Seq A and Seq B are reverse repeats to each other. 
> >>
> >>BLAST does not align A and B. 
> >>
> >>I can manipulate the sequences by reversing one seq and then 
> >>align, but I'd
> >>like to know whether there is a program that align A and B 
> >>without extra
> >>sequence manipulation. Any information is appreciated.
> >>_______________________________________________
> >>BiO_Bulletin_Board maillist  -  
> BiO_Bulletin_Board at bioinformatics.org
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> >>
> > 
> > _______________________________________________
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> 
> -- 
> Martin Gollery
> Associate Director
> Center For Bioinformatics
> University of Nevada at Reno
> Dept. of Biochemistry / MS330
> 775-784-7042
> -----------
> Marty's Law- the number of Bioinformatics acronyms will 
> double every 18 
> months.
> _______________________________________________
> BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> 



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