插入片段查找--isfinder

This database provides a list of insertion sequences isolated from eubacteria and archae. It is organised into individual files containing their general features (name, size, origin, family…..) as well as their DNA and potential protein sequences. Although most of the entries have been identified as individual elements, a growing number are included from their description in sequenced bacterial genomes.

The search engine permits the retrieval and display of individual and groups of ISs based on a combination of their general features.

Two levels of search are available. The simple search option enables the user to sort elements using a limited number of basic items whereas the extensive search offers an additional set of possibilities such as comparisons of the sequences of terminal inverted repeats and a variety of different layout displays. Built in links are provided to: the EMBL sequence database, the NCBI taxonomy database and to the ESF plasmid database.

At present, only individual sequences can be downloaded one by one for comparison. An on-line BLAST facility is available and in future versions direct access to additional analytical tools will be provided on line.

Permission: It is not permitted to download the ISfinder database without written authorization. Moreover, it is also not permitted at any time to distribute the database to third parties either individually or as part of web-based software.

寻找你基因组里面的IS 点击上方界面using the database,会出现search,analysis,submit,选择analysis,上传你的基因组,选择blast的方式,这样你的上传序列会跟IS数据库比对,得到你基因组中的IS序列

官网:https://www-is.biotoul.fr//

问题:在文献里面看到的是一个基因组里面找到了37个IS,但是我的基因组里有貌似有上百个,寻找IS的工具是Blbast,这里的阈值scores,和E-value应该设置多少才合适呢??默认是10?

个人公众号,比较懒,很少更新,可以在上面提问题:

更多精彩,请移步公众号阅读:

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专注生物信息 专注转化医学