答复: [BiO BB] Where can I make Logo plot?

ekeen ekeen at tongji.edu.cn
Mon Aug 15 09:21:24 EDT 2005


Thanks Sam et al.
I have done it with your help. :)


-----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 Samantha Fox
发送时间: 2005年8月15日 6:48
收件人: The general forum at Bioinformatics.Org
主题: Re: [BiO BB] Where can I make Logo plot?

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? 
> 
>   
> 
>   
> 
>   
> 
> ./I 
> 
>   
> 
> Samantha Fox wrote: 
> 
>   
> 
> >Thanks so much for your replies. However, it did not work yet. cd-hit 
> 
> >gave this error, and blastclust is not usable for such small sequences 
> 
> >! 
> 
> >  
> 
> >Any suggestions ? 
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> >  
> 
> >  
> 
> >  
> 
> >>cat fasta 
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> >>one 
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> >>    
> 
> >>  
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> >tagcgc 
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> >  
> 
> >  
> 
> >>two 
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> >>    
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> >>  
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> >atcgtt 
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> >  
> 
> >  
> 
> >>./cd-hit -i fasta -o www 
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> >>    
> 
> >>  
> 
> >total seq: 0 
> 
> >longest and shortest : 0 and 99999 
> 
> >Total letters: 0 
> 
> >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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> >>./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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> >  
> 
> >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 
> 
> >>word size is 32. 
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> >>  
> 
> >>Marty 
> 
> >>  
> 
> >>On 8/9/05, Marcos Oliveira de Carvalho <operon at cbiot.ufrgs.br> wrote: 
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> >>    
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> >>  
> 
> >>>Hi Samantha, 
> 
> >>>  
> 
> >>>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:

> 
> >>>ftp://ftp.ncbi.nih.gov/blast/ 
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> >>>  
> 
> >>>cheers 
> 
> >>>Marcos 
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> >>>  
> 
> >>>  
> 
> >>>  
> 
> >>>On Tue, 09 Aug 2005 14:24:41 -0300, Samantha Fox <bioinfosm at gmail.com> 
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> >>>wrote: 
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> >>>  
> 
> >>>      
> 
> >>>  
> 
> >>>>Hi, 
> 
> >>>>  
> 
> >>>>I have a set of small DNA sequences (about 40) 6-10 bp, and wish to 
> 
> >>>>group them into clusters based on sequence. 
> 
> >>>>  
> 
> >>>>Any suggestions for doing that ? 
> 
> >>>>  
> 
> >>>>Thanks, 
> 
> >>>>  
> 
> >>>>Samantha 
> 
> >>>>        
> 
> >>>>  
> 
> >_______________________________________________ 
> 
> >Bioinformatics.Org general forum  - 
> BiO_Bulletin_Board at bioinformatics.org 
> 
> >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
> 
> >  
> 
> >  
> 
> >  
> 
> >  
> 
>   
> 
>   
> 
> -- 
> 
>   
> 
> 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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