Anybody familiar with genome assembly software? - 未名空间MITBBS历史存档

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Anybody familiar with genome assembly software?

Anybody familiar with genome assembly software?# Biology - 生物学

K*42012-02-03 08:02

1 楼

Don't know exactly the word.
What I have is whole genome sequences for a new model organism. But the annotation hasn't been done. Does anyone know what software or package I should use to define its ORFs, cDNAs, and proteins? Is it easy to achieve?

P*62012-02-03 08:02

2 楼

http://genome.ucsc.edu/
不过你可能需要不少时间去熟悉这个网站或者其他软件，如果你要求的比较多的话。如
果在学校，上个bioinformatics的入门课会有帮助。这种经验性的东西不难，但是自己
找费时间。

annotation hasn't been done. Does anyone know what software or package I
should use to define its ORFs, cDNAs, and proteins? Is it easy to achieve?

【在 K**4 的大作中提到】

: Don't know exactly the word.
: What I have is whole genome sequences for a new model organism. But the annotation hasn't been done. Does anyone know what software or package I should use to define its ORFs, cDNAs, and proteins? Is it easy to achieve?

K*42012-02-03 08:02

3 楼

谢谢，但是这个database的数据都是已经注释好的了
我的数据是新测序的基因组序列，没有注释基因位置，我想知道怎么注释它
不知道这个工作量很大吗

【在 P*****6 的大作中提到】

: http://genome.ucsc.edu/
: 不过你可能需要不少时间去熟悉这个网站或者其他软件，如果你要求的比较多的话。如
: 果在学校，上个bioinformatics的入门课会有帮助。这种经验性的东西不难，但是自己
: 找费时间。
:
: annotation hasn't been done. Does anyone know what software or package I
: should use to define its ORFs, cDNAs, and proteins? Is it easy to achieve?

t*e2012-02-03 08:02

4 楼

bowtie, tophat

l*12012-02-03 08:02

5 楼

try free gsMapper and gsAssembler
cited:
>Installation
Where can I get a copy of the GS-FLX Mapping and Assembly software
I wrote to Roche to ask if we could give copies to people, and they wrote
back to say it is license free for non-commercial usage, so if you need a
copy please go to web link:
//genepool.bio.ed.ac.uk/nextgenbug/faq/roche_454_gs_flx
and
for Bowtie and gsMapper
please refer:
cited
>The 454 reads may be a bit long for Bowtie. You would be better off using
the gsMapper software that Roche provides for 454 read mapping. If you don't
have it, you can write to Roche and request it.
//seqanswers.com/forums/showthread.php?t=5082
if you still can not fix all by yourself please contact to below possible mentor:
//igfl.ens-lyon.fr/equipes/genomique-du-developpement-et-evolution-a.-khila
//arthropodgenomes.org/wiki/Abderrahman_Khila

【在 K**4 的大作中提到】

: 谢谢，但是这个database的数据都是已经注释好的了
: 我的数据是新测序的基因组序列，没有注释基因位置，我想知道怎么注释它
: 不知道这个工作量很大吗