InterProScan, Conserved domain database, SMART and PFAM
Hello guys
Quick question,
I trying to scan for some specific domains and others if present in protein of interest. I used InterProscan, but InterProScan did not predict all the domains. However, when I scan this proteins in PFAM and SMART I find these domains. Based on my knowledge InterProScan also include database such PFAM, SMART and Conserved domain database. How come I am not able to predict them when using InterProScan, whereas if I am using for example PFAM directly I get them.
Thanks in advance
• 1,558 views
•
link
updated
by
Ram
•
written
by
lukhanyomakhabane •
•
written
by
lukhanyomakhabane •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How to detect divergent domains in AlphaFold models (CDD/InterProscan not working, PyMOL alignment)
written by LLG •
-
Software to draw protein domains of proteins
written by lukhanyomakhabane •
-
Extract domain sequence from whole protein sequence
written by carlosmunozm •
-
Get integrated coordinates in InterProScan output
written by svet.sidorov
-
Find all domains in a list of proteins
written by dugong •
-
size (how many amino acids) are cytosolic or extracellular in membrane protein
written by mabohawya •
-
extracting domain regions from PDB
written by a.abnousi •
-
Difference between the PFam domain information from UCSC and PDB site
written by ChIP
-
Cutting Off The First Domain From All The Proteins In An Alignment
written by khorms
-
How Can I Efficiently Parse Hmmer Results To Find Listed Domains And Their Architecture?
written by James Ashmore •
it is very well likely that Interproscan uses different thresholds (compared to what the individual DBs do) which could indeed result in domains being present/absent .
However, it would be very surprising if those domains score high, aka they are more likely to be borderline/grey zone matches