[BiO BB] Where can I make Logo plot?

[Samantha Fox]

type seqlogo in url bar .... and hit enter .. its the berkley tool
Google for Sequence logo plot, you can find other options as well.

Sam

On 8/10/05, ekeen <ekeen at tongji.edu.cn> wrote:
>  
>  
> 
> Where can I make Logo plot like follow? 
> 
> Thanks. 
> 
>  
> 
> -----邮件原件-----
>  发件人:
> bio_bulletin_board-bounces+ekeen=tongji.edu.cn at bioinformatics.org
> [mailto:bio_bulletin_board-bounces+ekeen=tongji.edu.cn at bioinformatics.org]
> 代表 Iddo Friedberg
>  发送时间: 2005年8月10日 6:12
>  收件人: The general forum at Bioinformatics.Org
>  主题: Re: [BiO BB] Clustering small DNA sequences into groups 
> 
>   
> 
> How about building a distance matrix of your own (based on %ID between 
> 
> fragments) and then use WEKA for the clustering? 
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>   
> 
>   
> 
>   
> 
> ./I 
> 
>   
> 
> Samantha Fox wrote: 
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>   
> 
> >Thanks so much for your replies. However, it did not work yet. cd-hit 
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> >gave this error, and blastclust is not usable for such small sequences 
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> >! 
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> >  
> 
> >Any suggestions ? 
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> >  
> 
> >  
> 
> >  
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> >>cat fasta 
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> >>one 
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> >>    
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> >>  
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> >tagcgc 
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> >  
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> >  
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> >>two 
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> >>    
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> >>  
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> >atcgtt 
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> >  
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> >  
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> >>./cd-hit -i fasta -o www 
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> >>    
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> >>  
> 
> >total seq: 0 
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> >longest and shortest : 0 and 99999 
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> >Total letters: 0 
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> >terminate called after throwing an instance of 'std::bad_alloc' 
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> >  what():  St9bad_alloc 
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> >Abort (core dumped) 
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> >  
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> >  
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> >  
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> >>./cd-hit -i fasta -o www -l 5 
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> >>    
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> >>  
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> >  
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> >Fatal Error 
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> >Too short -l, redefine it 
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> >  
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> >Program halted !! 
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> >  
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> >  
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> >  
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> >On 8/9/05, Martin Gollery <marty.gollery at gmail.com> wrote: 
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> >  
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> >  
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> >>I believe those sequences are too short for Blastclust. The default 
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> >>word size is 32. 
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> >>  
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> >>Marty 
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> >>  
> 
> >>On 8/9/05, Marcos Oliveira de Carvalho <operon at cbiot.ufrgs.br> wrote: 
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> >>    
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> >>  
> 
> >>>Hi Samantha, 
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> >>>  
> 
> >>>BLASTCLUST can group DNA sequences. Maybe you will need to tweak the 
> 
> >>>parameters (almost the same for BLAST). You can get it at the NCBI ftp: 
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> >>>ftp://ftp.ncbi.nih.gov/blast/ 
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> >>>  
> 
> >>>cheers 
> 
> >>>Marcos 
> 
> >>>  
> 
> >>>  
> 
> >>>  
> 
> >>>On Tue, 09 Aug 2005 14:24:41 -0300, Samantha Fox <bioinfosm at gmail.com> 
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> >>>wrote: 
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> >>>  
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> >>>      
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> >>>  
> 
> >>>>Hi, 
> 
> >>>>  
> 
> >>>>I have a set of small DNA sequences (about 40) 6-10 bp, and wish to 
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> >>>>group them into clusters based on sequence. 
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> >>>>  
> 
> >>>>Any suggestions for doing that ? 
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> >>>>  
> 
> >>>>Thanks, 
> 
> >>>>  
> 
> >>>>Samantha 
> 
> >>>>        
> 
> >>>>  
> 
> >_______________________________________________ 
> 
> >Bioinformatics.Org general forum  - 
> BiO_Bulletin_Board at bioinformatics.org 
> 
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> 
> >  
> 
> >  
> 
> >  
> 
> >  
> 
>   
> 
>   
> 
> -- 
> 
>   
> 
> Iddo Friedberg, Ph.D. 
> 
> The Burnham Institute 
> 
> 10901 N. Torrey Pines Rd. 
> 
> La Jolla, CA 92037 
> 
> Tel: (858) 646 3100 x3516 
> 
> Fax: (858) 713 9930 
> 
> http://ffas.ljcrf.edu/~iddo 
> 
>   
> 
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