发信人: golem (狗愣), 信区: Biology
标 题: Re: Comment on draft sequence of rice
发信站: The unknown SPACE (Mon Apr 8 20:40:36 2002) WWW-POST

俺老板说，当年群魔聚会某地瓜分水稻chromosome的时候，各个国家针对自己的国情是有
所偏爱的。后果是，有的国家钱充分点儿，政府重视嘛，就先完成了自己的quota，有些
不象话的国家只要拿到自己感兴趣的部分就几乎停止进程，别的国家还不好意思催它，于
是就有了这个拖拖拉拉的Rice Genome Project。按说至少从98年开始的吧，到现在还没
拿出东西来，什么原因在里面？大家可想而知。
另外提一下，这种draft的genome也被称为dirty project，因为不确定性和错误机率都挺
大，难度比真正的gap free的database(比如Abrabidopsis)不可同日而语。
【 在 Marble (小石头哥哥) 的大作中提到: 】
: The collaborative work on draft sequnce of a subspecies of
: rice cultivated in China has just been published on Science.
: and you may notice the article followed by is draft sequece
: of another subspecies cultivated in Japan from another group.
: in my opinion, the work is very excellent. i can expect that
: the citations of the publication will increase dramatically
: in the near future. and it has significance in investigating
: breeding and cultivation of rice for production of more food.
: meanwhile, with more plant genomes available, it is beneficial
: to future work in many fileds, including plant physiology,
: plant pathology, biochemistry, phylogenetics, etc. in this
: sense, it is very admirable work completed primarily by China.
: from the paper per se, they generate a draft sequence of the
: 93-11 subspecies at 4X coverage. "whole-genome shotgun" approach
: is used to generat the DNA clones for sequencing. during
: assembling, they used the software they developed RePS to compute
: the frequence of 20bp sequence, which does not have any biological
: meaning. i think if the sequence appears in the genome upon
: certain threshold, then it gets a "finger". hehe. well, in
: another word, if it shows up too many times, then it is defined
: as repetitive sequence. only those that appear under certain
: threshold get positive value in assembly (i do not know the
: threshold value yet i know it affects the accuracy). then for
: the masked part where the repeats show often, gap-closure is
: required by available BACs, though there are still some gaps
: that are not filled. and then the next step is to construct the
: scaffold. (i have to mention that mtDNA, chloroDNA etc have
: not been considered). to address the quality, the authors got
: all available sequence-tagged sites (STSs, they are sort of
: lucky since it has already been generated along all the rice
: genome as genetic markers), full-length cDNA as well as their
: own homemade ESTs (MADE IN CHINA). so average functional
: coverage is 92.0%. they mentioned that the quality controls
: need contiguity on the length scale of a gene, single-base
: error as well as contig assembly accuracy ... blah blah blah.
: they also admit that there are still work need to be done
: to fill the gaps and check the construction. technically,
: the work requires construction of the clones, miniprep and
: sequencing, database, softwares for datamining and analysis,
: ... it is really a lot of work. i do not know much about the
: computer part, but at least i know it takes time to do 3.75
: million times of miniprep. so i was joking when i emailed
: some of the authors who were my classmates to ask them how
: many undergraduate they hired for such work and gave the kids
: a sense of honor doing sth great.
: back to the result, the following part is crude analysis of the
: draft sequence. first of all, they compared the GC contents
: of the rice genome with A. thaliana, and high GC contents was
: found that was bound within genes, many but not a few genes.
: then they analyzed the genic and intergenic DNA and estimated

--
一个人只拥有今生今世是不够的,他还应该拥有诗意的世界.

※ 来源:．The unknown SPACE bbs.mit.edu．[FROM: 128.8.21.129]