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BLAST and FASTQ dataset

热度 1已有 628 次阅读2013-2-13 02:44 PM |

need help for this subject. below are the initial discussions. 
if you have other helping ideas, we can discuss in this thread.

panda: anyone know BLAST and FASTQ dataset format so I can ask questions?
  • 老头乐: 没听说过,但你有问题尽管问。。 (2-12 20:58) 回复 删除
  • panda: in need import NCBI NT database (nucleotide sequence/DNA) into  mysql tables so I can match my testing/unknown sequence against the NT database (2-13 01:18) 回复 删除
  • 老头乐: 笨办法是先export, 再import...一听就是笨MM。。 (2-13 05:50) 回复 删除
  • panda: "export" from where? (2-13 13:19) 回复 删除
  • waspking: NCBI genbank stuff? heard of fastq from my postdoc (2-12 21:03) 回复 删除
  • panda: would you ask your postdoc if he knew how to import NCBI NT database (nucleotide sequence/DNA) into  mysql tables ? I don't have money for it now, but if I could get it work, there is a lot money (2-13 01:24) 回复 删除
  • deepocean: 国宝原来是生物系MM啊? (2-13 02:23) 回复 删除
  • waspking: he is gone. I always though panda is a male    you should be able to save the data in such a format to be compatible with mysql so it can be done automatically?  I am sure this has been done (2-13 12:37) 回复 删除
  • panda: yes, and I am 18 (2-13 13:17) 回复 删除
  • panda: "save the data" from where? (2-13 13:18) 回复 删除
  • waspking: you can download from NCBI. (2-13 13:22) 回复 删除
  • panda: links? (2-13 13:23) 回复 删除
  • waspking: c: http://researchremix.wordpress.com/2008/08/15/importing-pubmed-medline-details-into-mysql-database/ (2-13 13:23) 回复 删除
  • waspking: http://www.biostars.org/p/14382/ (2-13 13:24) 回复 删除
  • waspking: downloading: http://www.ncbi.nlm.nih.gov/guide/howto/dwn-records/ (2-13 13:25) 回复 删除
  • waspking: download by ftp: http://www.ncbi.nlm.nih.gov/Ftp/ (2-13 13:26) 回复 删除
  • panda: thanks. seems a PubChem link. I am actually looking for BLAST DB in here http://www.ncbi.nlm.nih.gov/Ftp/ (2-13 13:36) 回复 删除

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发表评论 评论 (2 个评论)

回复 昨夜雨 2013-2-13 04:09 PM
印象中BLAST DB都是用text strings, 用的是regular expression来检验。和关系数据库没有多大的关系。
回复 panda 2013-2-13 06:07 PM
昨夜雨: 印象中BLAST DB都是用text strings, 用的是regular expression来检验。和关系数据库没有多大的关系。
that is what I heard too. but in my experience, I can do much faster SQL regex in the data size like BLAST (50 GB the most?)

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