Monday, May 6, 2013

Configure FASTA database in PEAKS

Configuring FASTA databases in PEAKS is fairly easy especially if the FASTA file has the same header format as one of the public databases (e.g. NR, Swiss-Prot, IPI). It is just a matter of selecting the pre-defined format and the parsing rules will be automatically filled in.

There are also a large number of users use PEAKS to search on their in-house, customized FASTA databases. In this situation, the header format is very hard to predict and it varies case by case.

In PEAKS, the parsing rule is defined using regular expression. While regular expression is very powerful, it will take people quite a bit of time to master it. Since we got tons of searches to run every week, against FASTA files with so many different header formats, I created this lazy, generic parsing rule for internal use and in most cases, it worked good enough.

Accession. The regular expression tries to use everything before the first white space as the accession. If no white space were found within the first 30 characters, the first 30 characters will be used as accession.
>\([^\s|]{1,30}\)
Description. The whole line after ">" will be used as the description.
>\(.*\)



7 comments:

  1. إذا كنت تبحث عن عروض بأسعار معقولة ، فقد تحتاج أيضًا إلى شحن مجاني ، حيث يمكن أن تكون ضخمة ومكلفة لشحنها. لا مزيد من البحث عن U-Pack Box Store. لدينا أنواع متعددة من البطانيات المتحركة ، بكميات مختلفة ، كل ذلك مع الشحن المجاني.شركة نقل اثاث
    شركة نقل عفش بالخرج

    ReplyDelete
  2. This blog is what I was looking for. This piece of content will really help me. Thanks for sharing it. Coffee And Tea Wholesalers

    ReplyDelete
  3. After study a few of the blog posts on your website now, and I truly like your way of blogging. I bookmarked it to my bookmark website list and will be checking back soon. Pls check out my web site as well and let me know what you think.

    Forum.ppr.pl
    Information
    Click Here
    Visit Web

    ReplyDelete
  4. My name is Jams root, And I am a student. Today I am searching for a new topic for my work. And I use the taxation law assignment service service for completing it. And I see in your blog you talk about Configure FASTA database in PEAKS. It is a good topic. you wrote very well and described it. It helps many children. Thanks for sharing this blog with us

    ReplyDelete
  5. For those looking to enhance their bioinformatics tools, Hydrogen Executor offers a cutting-edge solution that seamlessly integrates with software like PEAKS for efficient database management and analysis.

    ReplyDelete
  6. Configuring FASTA database in PEAKS mirrors the meticulous setup required for accurate data interpretation. Similarly, a Progressive Healthcare Solutions LLC ensures precision in healthcare solutions. Whether in bioinformatics or medical diagnostics, both strive for excellence, highlighting the importance of reliable systems for success in diverse fields.

    ReplyDelete