[BiO BB] Where can I make Logo plot?

ekeen ekeen at tongji.edu.cn
Wed Aug 10 09:11:25 EDT 2005


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 ? 

> 

>  

> 

>>cat fasta

>>one

>>    

>> 

>tagcgc

>  

> 

>>two

>>    

>> 

>atcgtt

>  

> 

>>./cd-hit -i fasta -o www

>>    

>> 

>total seq: 0

>longest and shortest : 0 and 99999

>Total letters: 0

>terminate called after throwing an instance of 'std::bad_alloc'

>  what():  St9bad_alloc

>Abort (core dumped)

> 

>  

> 

>>./cd-hit -i fasta -o www -l 5

>>    

>> 

> 

>Fatal Error

>Too short -l, redefine it

> 

>Program halted !!

> 

> 

> 

>On 8/9/05, Martin Gollery <marty.gollery at gmail.com> wrote:

>  

> 

>>I believe those sequences are too short for Blastclust. The default

>>word size is 32.

>> 

>>Marty

>> 

>>On 8/9/05, Marcos Oliveira de Carvalho <operon at cbiot.ufrgs.br> wrote:

>>    

>> 

>>>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/

>>> 

>>>cheers

>>>Marcos

>>> 

>>> 

>>> 

>>>On Tue, 09 Aug 2005 14:24:41 -0300, Samantha Fox <bioinfosm at gmail.com>

>>>wrote:

>>> 

>>>      

>>> 

>>>>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

>>>>        

>>>> 

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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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