Protein Domain Architecture >> Shape And Colours

Question

[inadamj]

Hello every one, currently I am coding a program that draw the protein with its domains But I have an issue which is the domain shape and colour. There is overlapping between the domains and I do not know how to distinguish between the domains in order to specify the shape or the colour for each domain.

For example the input file is : A_acidus_CBS_106_47_iprscan.out From: http://www.aspergillusgenome.org/download/domains/A_acidus_CBS_106_47/A_acidus_CBS_106_47_iprscan.out

This tab-delimited text file contains the output of a search of all translated ORF sequences from this strain using the IprScan program.

Columns:

1. Systematic identifier of the input sequence
2. crc64 (unique checksum) of the sequence
3. Length of the sequence (in amino acids)
4. Analysis method
5. Source database entry for this match
6. Source database description for the entry
7. Start coordinate of the domain match
8. End coordinate of the domain match
9. E-value of the match (reported by analysis method)
10. Status of the match (T: true; ?: unknown)
11. Date of the IprScan run
12. InterPro domain identifier
13. InterPro domain description
14. GO (gene ontology) description for the InterPro domain

I want to know how to distinguish between them then after that I can give the user the choice to choose the shape and colour from the beginning.

Answer 1

[David Westergaard]

Most likely there is not an overlap between the biological domains. I suggest you study the InterPro page, try to do a few queries. InterPro is a collection of, primarily, Hidden Markov Models from different databases (e.g. PfamA, TIGRFAM, SUPERFAMILY.) The different model files for the same domains may vary a bit from database to database, depending on the seed alignment. That being said, there may be some cases where domains overlap found from models in the same database may overlap. I suggest you study these.

[inadamj]

thanks @David for answering .. the thing is the overlapping is available. I just need a source that tell me what is the available domains and their names so I can make sure while coding my program..

[David Westergaard]

I don't understand what you're trying to achieve, but if you go to the InterPro page, click "Download", The "Entry list" download should have what you are describing.