Protdraw Wiki

Create portable, flexible domain drawings of protein sequences

Status: Alpha

Brought to you by: chitistone, janetsmith

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---+ ProtDraw

ProtDraw creates flexible, organized, aesthetically pleasing and portable illustrations of the domain structures of input sequences.

This example shows a Protdraw rendering of fungal-specific RIM15 protein kinases from seven dermatophyte species. RIM15 is a metabolic reprogramming switch

---+++ Overview

Flow Chart [[%ATTACHURL%/protdraw.pdf][protdraw.pdf]]: Flow diagram for makeprotdraw and protdraw with input/output examples

---+++ Instructions for use

ProtDrawMain - present protein sequences and their domains in an aesthetically pleasing graphic format. Write results in postscript format for use by other graphics programs
Screen Shot [[%ATTACHURL%/protdraw_screenshot.tiff][protdraw_screenshot.tiff]]: Screen Shot of Protdraw session
MakeProtdraw - automatically prepare a Protdraw input file
- Runs HMMsearch on a protein fasta based on list of HMMs ( e.g. Pfam25). Picks the highest-scoring HMM if there are overlaps, and writes the results in the format read by ProtDraw
- Makes a table of sequences and their domain hits.
AdobeIllustrator - AI settings that work well on ProtDraw outfiles

---+++ Examples

---++++ Gene family analysis

---++++ Develop databases for automated functional annotation

Kinomics: [[%ATTACHURL%/apk.pdf][apk.pdf]]: Atypical protein kinases from KinBase : In this example makeprotdraw and protdraw were run on all of the atypical protein kinases at kinase.com vs all of Pfam25. Many of the domains in the drawing overlap other domains, but makeprotdraw selects only the best one for display in protdraw. %BLUE%This helps to identify the Pfam domain that best maps to the particular kinase family%BLACK%. The image itself was created by writing out a *ps file from protdraw, and opening it in adobe illustrator. The suffixes of the gene names refer to species: Hs, human;Mm, mouse; Dm, fly; Ce, worm; Aq, sponge; Sp, sea urchin; Sc, Yeast; Dd, Dicty; Sm, club moss, Cc, C. cinerea.
CAZy: [[%ATTACHURL%/CBM10_GH13_01.pdf][CBM10_GH13_01.pdf]]: Domain drawings of CBM10 through GH13 family members from our CAZy database, members with more than one CAZy classification :
- Work on this may be found in ==/seq/annotation/scripts/kinomics/cazy/nshenoy/protdraw/large_multifamilies==
- CAZY example CBM41, CMB48 and GH13:

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