finding matching motifs in a sequence and their position

Question

I am trying to find some matching motifs on a sequence, as well as the position that the motif is located in and then output that into a fasta file. The code below shows that the motif [L*L*L] is present in the sequence, when I run it returns as "YES" but I do not know where it is positioned.

peptide1="MKFSNEVVHKSMNITEDCSALTGALLKYSTDKSNMNFETLYRDAAVESPQHEVSNESGSTLKEHDYFGLSEVSSSNSSSGKQPEKCCREELNLNESATTLQLGPPAAVKPSGHADGADAHDEGAGPENPAKRPAHHMQQESLADGRKAAAEMGSFKIQRKNILEEFRAMKAQAHMTKSPKPVHTMQHNMHASFSGAQMAFGGAKNNGVKRVFSEAVGGNHIAASGVGVGVREGNDDVSRCEEMNGTEQLDLKVHLPKGMGMARMAPVSGGQNGSAWRNLSFDNMQGPLNPFFRKSLVSKMPVPDGGDSSANASNDCANRKGMVASPSVQPPPAQNQTVGWPPVKNFNKMNTPAPPASTPARACPSVQRKGASTSSSGNLVKIYMDGVPFGRKVDLKTNDSYDKLYSMLEDMFQQYISGQYCGGRSSSSGESHWVASSRKLNFLEGSEYVLIYEDHEGDSMLVGDVPWELFVNAVKRLRIMKGSEQVNLAPKNADPTKVQVAVG"

if re.search(r"L*L*L", peptide1):
    print("YES")
else: 
    print("NO")

The code that I wrote to find the position is below, but when I run it says invalid syntax. Could you please assist as I am still new in Bioinformatics, and I have no clue whether in the right track or not.

for position in range(len(peptide1)):
    if peptide1[position:].startswith(re.search(r"L*L*L")):
        print(position+1)

Lastly once the position of these motifs has been identified, how do I highlight them such that they are visible in the output fasta file.

I am searching for LxLxL where x can be any amino acid. I used the * to indicate to python that it should use any amino acid, but I think I am incorrect. Could you please assist on how I should actually be writing that motif?

Answer 1

re.search method do not return a simply boolean but a useful object contains many information:

#! /usr/bin/env python3

import re

peptide1="MKFSNEVVHKSMNITEDCSALTGALLKYSTDKSNMNFETLYRDAAVESPQHEVSNESGSTLKEHDYFGLSEVSSSNSSSGKQPEKCCREELNLNESATTLQLGPPAAVKPSGHADGADAHDEGAGPENPAKRPAHHMQQESLADGRKAAAEMGSFKIQRKNILEEFRAMKAQAHMTKSPKPVHTMQHNMHASFSGAQMAFGGAKNNGVKRVFSEAVGGNHIAASGVGVGVREGNDDVSRCEEMNGTEQLDLKVHLPKGMGMARMAPVSGGQNGSAWRNLSFDNMQGPLNPFFRKSLVSKMPVPDGGDSSANASNDCANRKGMVASPSVQPPPAQNQTVGWPPVKNFNKMNTPAPPASTPARACPSVQRKGASTSSSGNLVKIYMDGVPFGRKVDLKTNDSYDKLYSMLEDMFQQYISGQYCGGRSSSSGESHWVASSRKLNFLEGSEYVLIYEDHEGDSMLVGDVPWELFVNAVKRLRIMKGSEQVNLAPKNADPTKVQVAVG"

re_search_result = re.search(r'L*L*L', peptide1)
if re_search_result:
    print("YES")
    motif_start_position=re_search_result.start()
    motif_end_position=re_search_result.end()
    motif_length = re_search_result.end() - re_search_result.start()
    print("Motif start at position: %d" % motif_start_position)
    print("Motif end at position  : %d" % motif_end_position)
    print("SO length is ......... : %d" % motif_length)
    print("The motif is : <%s>" % peptide1[motif_start_position:motif_end_position])
else:
    print("NO")

Result is:

YES
Motif start at position: 20
Motif end at position  : 488
SO length is ......... : 468
The motif is : <LTGALLKYSTDKSNMNFETLYRDAAVESPQHEVSNESGSTLKEHDYFGLSEVSSSNSSSGKQPEKCCREELNLNESATTLQLGPPAAVKPSGHADGADAHDEGAGPENPAKRPAHHMQQESLADGRKAAAEMGSFKIQRKNILEEFRAMKAQAHMTKSPKPVHTMQHNMHASFSGAQMAFGGAKNNGVKRVFSEAVGGNHIAASGVGVGVREGNDDVSRCEEMNGTEQLDLKVHLPKGMGMARMAPVSGGQNGSAWRNLSFDNMQGPLNPFFRKSLVSKMPVPDGGDSSANASNDCANRKGMVASPSVQPPPAQNQTVGWPPVKNFNKMNTPAPPASTPARACPSVQRKGASTSSSGNLVKIYMDGVPFGRKVDLKTNDSYDKLYSMLEDMFQQYISGQYCGGRSSSSGESHWVASSRKLNFLEGSEYVLIYEDHEGDSMLVGDVPWELFVNAVKRLRIMKGSEQVNL>

The motif L*L*L is a quite strange: L zero or many times followed by L zero or many times followed by followed by a L. It's an equivalent of L*L, equivalent of L+.

Do you search for L.*L.*L, L[^L]*L[^L]*L or simply LLL ?

Notes:

• When you post code, use block delimited by two ``` (no by two simple `)
• In Python, code indentation is very important, always use spaces (4)

---

If you want to loop over all motifs (like strings), use findall method:

#! /usr/bin/env python3

import re

peptide1="MKFSNEVVHKSMNITEDCSALTGALLKYSTDKSNMNFETLYRDAAVESPQHEVSNESGSTLKEHDYFGLSEVSSSNSSSGKQPEKCCREELNLNESATTLQLGPPAAVKPSGHADGADAHDEGAGPENPAKRPAHHMQQESLADGRKAAAEMGSFKIQRKNILEEFRAMKAQAHMTKSPKPVHTMQHNMHASFSGAQMAFGGAKNNGVKRVFSEAVGGNHIAASGVGVGVREGNDDVSRCEEMNGTEQLDLKVHLPKGMGMARMAPVSGGQNGSAWRNLSFDNMQGPLNPFFRKSLVSKMPVPDGGDSSANASNDCANRKGMVASPSVQPPPAQNQTVGWPPVKNFNKMNTPAPPASTPARACPSVQRKGASTSSSGNLVKIYMDGVPFGRKVDLKTNDSYDKLYSMLEDMFQQYISGQYCGGRSSSSGESHWVASSRKLNFLEGSEYVLIYEDHEGDSMLVGDVPWELFVNAVKRLRIMKGSEQVNLAPKNADPTKVQVAVG"

re_findall_result = re.findall(r'L[^L]*L[^L]*L', peptide1)
for element in re_findall_result:
    print("Element: <%s>" % element)

Result will be:

Element: <LTGALL>
Element: <LYRDAAVESPQHEVSNESGSTLKEHDYFGL>
Element: <LNLNESATTL>
Element: <LGPPAAVKPSGHADGADAHDEGAGPENPAKRPAHHMQQESLADGRKAAAEMGSFKIQRKNIL>
Element: <LDLKVHL>
Element: <LSFDNMQGPLNPFFRKSL>
Element: <LVKIYMDGVPFGRKVDLKTNDSYDKL>
Element: <LEDMFQQYISGQYCGGRSSSSGESHWVASSRKLNFL>
Element: <LIYEDHEGDSMLVGDVPWEL>

---

If you want all find objects like with search method, use finditer method:

#! /usr/bin/env python3

import re

peptide1="MKFSNEVVHKSMNITEDCSALTGALLKYSTDKSNMNFETLYRDAAVESPQHEVSNESGSTLKEHDYFGLSEVSSSNSSSGKQPEKCCREELNLNESATTLQLGPPAAVKPSGHADGADAHDEGAGPENPAKRPAHHMQQESLADGRKAAAEMGSFKIQRKNILEEFRAMKAQAHMTKSPKPVHTMQHNMHASFSGAQMAFGGAKNNGVKRVFSEAVGGNHIAASGVGVGVREGNDDVSRCEEMNGTEQLDLKVHLPKGMGMARMAPVSGGQNGSAWRNLSFDNMQGPLNPFFRKSLVSKMPVPDGGDSSANASNDCANRKGMVASPSVQPPPAQNQTVGWPPVKNFNKMNTPAPPASTPARACPSVQRKGASTSSSGNLVKIYMDGVPFGRKVDLKTNDSYDKLYSMLEDMFQQYISGQYCGGRSSSSGESHWVASSRKLNFLEGSEYVLIYEDHEGDSMLVGDVPWELFVNAVKRLRIMKGSEQVNLAPKNADPTKVQVAVG"

re_findall_result = re.finditer(r'L[^L]*L[^L]*L', peptide1)
for element in re_findall_result:
    print("peptide1[%s:%s]=<%s>" % (element.start(), element.end(), peptide1[element.start():element.end()]))

Result will be:

peptide1[20:26]=<LTGALL>
peptide1[39:69]=<LYRDAAVESPQHEVSNESGSTLKEHDYFGL>
peptide1[90:100]=<LNLNESATTL>
peptide1[101:163]=<LGPPAAVKPSGHADGADAHDEGAGPENPAKRPAHHMQQESLADGRKAAAEMGSFKIQRKNIL>
peptide1[248:255]=<LDLKVHL>
peptide1[278:296]=<LSFDNMQGPLNPFFRKSL>
peptide1[378:404]=<LVKIYMDGVPFGRKVDLKTNDSYDKL>
peptide1[407:443]=<LEDMFQQYISGQYCGGRSSSSGESHWVASSRKLNFL>
peptide1[449:469]=<LIYEDHEGDSMLVGDVPWEL>