[BiO BB] Where can I make Logo plot?
Samantha Fox
bioinfosm at gmail.com
Sun Aug 14 18:47:56 EDT 2005
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:
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> Where can I make Logo plot like follow?
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> Thanks.
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> -----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
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>
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> How about building a distance matrix of your own (based on %ID between
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> fragments) and then use WEKA for the clustering?
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> ./I
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> 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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> >
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> >Any suggestions ?
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> >
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> >
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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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> >>
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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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> >>
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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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> >>
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> >>>Hi Samantha,
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> >>>
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> >>>BLASTCLUST can group DNA sequences. Maybe you will need to tweak the
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> >>>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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> >>>
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> >>>cheers
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> >>>Marcos
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> >>>
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> >>>
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> >>>
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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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> >>>
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> >>>
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> >>>
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> >>>>Hi,
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> >>>>
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> >>>>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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> >>>>
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> >>>>Any suggestions for doing that ?
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> >>>>
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> >>>>Thanks,
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> >>>>
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> >>>>Samantha
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> >>>>
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> >>>>
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> >_______________________________________________
>
> >Bioinformatics.Org general forum -
> BiO_Bulletin_Board at bioinformatics.org
>
> >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
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> >
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> >
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> >
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> >
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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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