1 / 6

EMBOSS (2)

EMBOSS (2). Dinesh Gupta ICGEB. Exercises. Are you able to run tfm ? Can you find a program to: Display multiple alignments. Find ORFs (Open Reading Frames). Translate a sequence. Find restriction enzyme sites Find the isoelectric point of a protein. Do global alignments.

tavia
Download Presentation

EMBOSS (2)

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. EMBOSS (2) Dinesh Gupta ICGEB

  2. Exercises • Are you able to run tfm ? • Can you find a program to: • Display multiple alignments. • Find ORFs (Open Reading Frames). • Translate a sequence. • Find restriction enzyme sites • Find the isoelectric point of a protein. • Do global alignments.

  3. Are you able to run:- • patmatdb: Search a protein sequence with motif • patmatmotifs: Search a PROSITE motif database with a protein database • remap: search rebase for enzyme

  4. Database installation • prosextract : prosite.dat is needed • Rebaseextract: rebase files are needed

  5. Working on multiple files • @file operator • writing batch scripts

  6. other variables • -sbegin sequence begin position • -send sequence end position • -sreverse reverse complement the sequence • -slower change sequence to lower case • -supper change sequence to upper case • -osformat output sequence format • -help show help • -options ask for optional parameters • -auto run silently (for use in scripts, e.g. perl)

More Related