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You may choose the example sequence (Insert example) provided in the form and SCANMOT motifs (Insert motifs) and search against 'nr' database of sequences with 30% relaxation for motifs and a minimum of 2 motifs to be present in the hits.

Step 1: Use insert example link to paste sequence
Paste the query sequence in fasta format( insert example )

Step 2: Use insert example link to paste motifs Paste Motifs Below
(In order which they appear in the query sequence) ( Insert example )

Order	Motifs
I
II
III
IV
V
VI
VII
VIII
IX
X

Click here to access a database of structural motifs for protein superfamilies.

Step 3: Choose "nr" form the drop down menu
Choose the database to search for motifs

OR
Create Custom Database by Pasting the sequences below
(Note: The motifs will be searched only in these sequences) Paste the sequences in fasta format

OR Upload Your file(database)-Sequences should be in fasta format

Wish to go for similar residue substitution?
eg: [F]=[FYW], [V]=[VIL], [D]=[DE], [H]=[HKR], [N]=[NQ], [C]=[CST], A=[AG]

Yes
No

Step 4: Choose "30%" Relaxation filter from the drop down menu

Choose Relaxation filter for motif spacer length between query and hit
(click here for details)

%
Step :5 Choose "2" as minimum number of motifs

Choose the minimum number of motifs that should be present in the hits
Atleast Motifs
Step :6 Press "Submit" button to iniate the process

Wish to go for PSI-BLAST search of your query and
mapping of the motifs by scanmot?
Click here

############### PROSITE| PROFILE| PRINTS| FINDMOTIF| PFAM| BLOCKS| PDB| SCOP ###############

Contacts:
Sowdhamini.R -mini@ncbs.res.in
Saikat Chakrabarti -saikat@ncbs.res.in
Pugalenthi.G -pugal(at)ncbs.res.in
Prem Anand. A -prem@ncbs.res.in
Nitin Bhardwaj -nitinb@che.iitb.ac.in