The document discusses regular expressions and provides examples of common regex patterns used for tasks like searching DNA sequences or scanning for protein domains. It then provides a sample of DNA/protein sequences and suggests using translated regex patterns to scan the sequences for specific consensus patterns representing protein domains.

2. FBW
24-10-2017
Wim Van Criekinge

3. Google Calendar
Louis Coussement

4. Recap
if condition:
statements
[elif condition:
statements] ...
else:
statements
while condition:
statements
for var in sequence:
statements
break
continue
Strings

5. Lists
• Flexible arrays, not Lisp-like linked
lists
• a = [99, "bottles of beer", ["on", "the",
"wall"]]
• Same operators as for strings
• a+b, a*3, a[0], a[-1], a[1:], len(a)
• Item and slice assignment
• a[0] = 98
• a[1:2] = ["bottles", "of", "beer"]
-> [98, "bottles", "of", "beer", ["on", "the", "wall"]]
• del a[-1] # -> [98, "bottles", "of", "beer"]

6. Dictionaries
• Hash tables, "associative arrays"
• d = {"duck": "eend", "water": "water"}
• Lookup:
• d["duck"] -> "eend"
• d["back"] # raises KeyError exception
• Delete, insert, overwrite:
• del d["water"] # {"duck": "eend", "back": "rug"}
• d["back"] = "rug" # {"duck": "eend", "back":
"rug"}
• d["duck"] = "duik" # {"duck": "duik", "back":
"rug"}

7. if condition:
statements
[elif condition:
statements] ...
else:
statements
while condition:
statements
for var in sequence:
statements
break
continue
Strings
REGULAR EXPRESSIONS

8. Regular Expression Quick Guide
^ Matches the beginning of a line
$ Matches the end of the line
. Matches any character
s Matches whitespace
S Matches any non-whitespace character
* Repeats a character zero or more times
*? Repeats a character zero or more times (non-greedy)
+ Repeats a chracter one or more times
+? Repeats a character one or more times (non-greedy)
[aeiou] Matches a single character in the listed set
[^XYZ] Matches a single character not in the listed set
[a-z0-9] The set of characters can include a range
( Indicates where string extraction is to start
) Indicates where string extraction is to end

9. Example
import re
dna = "ATCGCGAATTCAC"
if re.search(r"GAATTC", dna):
print("restriction site found!")

10. • Predict the fragment lengths that we will get
if we digest the sequence with two
restriction enzymes – EcoRI, whose
recognition site is G/AATTC alone.
• With BamHI, whose recognition site is
G/GATCG alone
• And when we do a double digest
• The forward slashes (/) in the recognition
sites represent the place where the
enzyme cuts the DNA.
• http://rebase.neb.com/rebase/rebase.html
Double digest

11. Double digest: DNA
• ATGGCAGGATCGATAACCCCCCGTTTCTACTTCTAGAGGAGAAAAGTATTGACATGAGCGCTCCC
GGCACAAGGGCCAAAGAAGTCTCCAATTTCTTATTTCCGAATGACATGCGTCTCCTTGCGGGTAAA
TCACCGACCGCAATTCATAGAAGCCTGGGGGAACAGATAGGAATTCGTCTAATTAGCTTAAGAGA
GTAAATCCTGGGATCATTCAGTAGTAACCATAAACTTACGCTGGGGCTTCTTCGGCGGATTTTTAC
AGTTACCAACCAGGAGATTTGAAGTAAATCAGTTGAGGATTTAGCCGCGCTATCCGGTAATCTCCA
AATTAAAACATACCGTTCCATGAAGGGATCGGCTAGAATTACTTACCGGCCTTTTCCATGCCTGCG
CTATACCCCCCCACTCTCCCGCTTATCCGTCCGAGCGGAGGCAGTGCGATCCTCCGTTAAGATATT
CTTACGTGTGACGTAGCTATGTATTTTGCAGAGCTGGCGAACGCGTTGAACACTTCACAGATGGTA
GGGATTCGGGTAAAGGGCGTATAATTGAATTCGGGGACTAACATAGGCGTAGACTACGATGGCGC
CAACTCAATCGCAGCTCGAGCGCCCTGAATAACGTACTCATCTCAACTCATTCTCGGCAATCTACC
GAGCGACTCGATTATCAACGGCTGTCTAGCAGTTCTAATCTTTTGCCAGCATCGTAATAGCCTCCA
AGAGATTGATGATAGCTATCGGCACAGAACTGAGACGGCGCCGATGGATAGCGGACTTTCGGTCA
ACCACAATTCCCCACGGGACAGGTCCTGCGGTGCGCATCACTCTGAATGTACAAGCAACCCAAGT
GGGCCGAGCCTGGACTCAGCTGGTTCGAATTCCTGCGTGAGCTCGAGACTCGGGATGACAGCTCTT
TAAACATAGAGCGGGGGCGTCGAACGGTCGAGAAAGTCATAGTACCTCGGGTACCAACTTACTCA
GGTTATTGCTTGAAGCTGTACTATTTTAGGGGGGGAGCGCTGAAGGTCTCTTCTTCTCATGACTGA
ACTCGCGAGGGTCGTGAAGTCGGTTCCTTCAATGGTTAAAAAACAAAGGATCGGGCTTACTGTGC
GCAGAGGAACGCCCATCTAGCGGCTGGCGTCTTGAATGCTCGGTCCCCTTTGTCATTCCGGATTAA
TCCATTTCCCTCATTCACGAGCTTGCGAAGTCTACATTGGTATATGAATGCGACCTAGAAGAGGGC
GCTTAAAATTGGCAGTGGTTGATGCTCTAAACTCCATTTGGTTTACTCGTGCATCACCGCGATAGG
CTGACAAAGGTTTAACATTGAATAGCAAGGCACTTCCGGTCTCAATGAACGGCCGGGAAAGGTAC
GCGCGCGGTATGGGAGGATCAAGGGGCCAATAGAGAGGCTCCTCTCTCACTCGCTAGGAGGCAAA
TGTGAATTCAAAACAATGGTTACTGCATCGATACATAAAACATGTCCATCGGTTGCCCAAAGTGTT
AAGTGTCTATCACCCCTAGGGCCGTTTCCCGCATATAAACGCCAGGTTGTATCCGCATTTGATGCT
ACCGTGGATGAGTCTGCGTCGAGCGCGCCGCACGAATGTTGCAATGTATTGCATGAGTAGGGTTG
ACTAAGAGCCGTTAGATGCGTCGCTGTACTAATAGTTGTCGACAGACCGTCGAGATTAGAAAATG
GTACCAGCATTTTCGGAGGTTCTCTAACTAGTATGGATTGCGGTGTCTTCACTGTGCTGCGGCTACC
CATCGCCTGAAATCCAGCTGGTGTCAAGCCATCCCCTCTCCGGGACGCCGCATGTAGTGAAACATA
TACGTTGCACGGGTTCACCGCGGTCCGTTCTGAGTCGACCAAGGACACAATCGAGCTCCGATCCGT
ACCCTCGACAAACTTGTACCCGACCCCCGGAGCTTGCCAGCTCCTCGGGTATCATGGAGCCTGTGG
TTCATCGCGTCCGATATCAAACTTCGTCATGATAAAGTCCCCCCCTCGGGAGTACCAGAGAAGATG
ACTACTGAGTTGTGCGAT GGATCG

12. Towards a protein prosite scanner
N-{P}-[ST]-{P}.
[RK](2)-x-[ST].
[ST]-x-[RK].
[ST]-x(2)-[DE].
[RK]-x(2,3)-[DE]-x(2,3)-Y.
G-{EDRKHPFYW}-x(2)-[STAGCN]-{P}.
x-G-[RK]-[RK].
C-x-[DN]-x(4)-[FY]-x-C-x-C.
E-x(2)-[ERK]-E-x-C-x(6)-[EDR]-x(10,11)-[FYA]-[YW].
[DEQGSTALMKRH]-[LIVMFYSTAC]-[GNQ]-[LIVMFYAG]-[DNEKHS]-S-[LIVMST]-{PCFY}-[STAGCPQLIVMF]-[LIVMATN]-[DENQGTAKRHLM]-[LIVMWSTA]-
[LIVGSTACR]-{LPIY}-{VY}-[LIVMFA].
[KRHQSA]-[DENQ]-E-L>.
R-G-D.
[AG]-x(4)-G-K-[ST].
D-{W}-[DNS]-{ILVFYW}-[DENSTG]-[DNQGHRK]-{GP}-[LIVMC]-[DENQSTAGC]-x(2)-[DE]-[LIVMFYW].
[EQ]-{LNYH}-x-[ATV]-[FY]-{LDAM}-{T}-W-{PG}-N.
[LIVM]-x-[SGNL]-[LIVMN]-[DAGHENRS]-[SAGPNVT]-x-[DNEAG]-[LIVM]-x-[DEAGQ]-x(4)-[LIVM]-x-[LM]-[SAG]-[LIVM]-[LIVMT]-[WS]-x(0,1)-[LIVM](2).
[FY]-C-[RH]-[NS]-x(7,8)-[WY]-C.
C-x-C-x(2)-{V}-x(2)-G-{C}-x-C.
C-x(2)-P-F-x-[FYWIV]-x(7)-C-x(8,10)-W-C-x(4)-[DNSR]-[FYW]-x(3,5)-[FYW]-x-[FYWI]-C.
[LIFAT]-{IL}-x(2)-W-x(2,3)-[PE]-x-{VF}-[LIVMFY]-[DENQS]-[STA]-[AV]-[LIVMFY].
[KRH]-x(2)-C-x-[FYPSTV]-x(3,4)-[ST]-x(3)-C-x(4)-C-C-[FYWH].
C-x(4,5)-C-C-S-x(2)-G-x-C-G-x(3,4)-[FYW]-C.
[LIVMFYG]-[ASLVR]-x(2)-[LIVMSTACN]-x-[LIVM]-{Y}-x(2)-{L}-[LIV]-[RKNQESTAIY]-[LIVFSTNKH]-W-[FYVC]-x-[NDQTAH]-x(5)-[RKNAIMW].
C-x(2,4)-C-x(3)-[LIVMFYWC]-x(8)-H-x(3,5)-H.
L-x(6)-L-x(6)-L-x(6)-L.
C-x(2)-C-x(1,2)-[DENAVSPHKQT]-x(5,6)-[HNY]-[FY]-x(4)-C-x(2)-C-x(2)-F(2)-x-R.
[LIVMFE]-[FY]-P-W-M-[KRQTA].
L-M-A-[EQ]-G-L-Y-N.
IRED_1R-P-C-x(11)-C-V-S.
[RKQ]-R-[LIM]-x-[LF]-G-[LIVMFY]-x-Q-x-[DNQ]-V-G.
[KR]-x(1,3)-[RKSAQ]-N-{VL}-x-[SAQ](2)-{L}-[RKTAENQ]-x-R-{S}-[RK].
[LIVMF](2)-D-E-A-D-[RKEN]-x-[LIVMFYGSTN].
[KRQ]-[LIVMA]-x(2)-[GSTALIV]-{FYWPGDN}-x(2)-[LIVMSA]-x(4,9)-[LIVMF]-x-{PLH}-[LIVMSTA]-[GSTACIL]-{GPK}-{F}-x-[GANQRF]-[LIVMFY]-x(4,5)-[LFY]-x(3)-
[FYIVA]-{FYWHCM}-{PGVI}-x(2)-[GSADENQKR]-x-[NSTAPKL]-[PARL].
Scan for the following prosite patterns in your 4 sequences
Hint: translate the patters to regexes and then scan

13. reuse galacto.py in github
Consensus_pattern="G-R-x-N-[LIV]-I-G-[DE]-H-x-D-Y"
pattern=Consensus_pattern.replace("-","")
pattern=pattern.replace("x","[A-Z]")
#print(pattern)
count=0
for s in sequences:
count=count+1
print ("searching seq",count)
s=s.replace(" ","")
matches = re.finditer(pattern,s)
for match in matches:
print (match.group(0),"from: ",match.start(),"to: ",match.end())

14. >SEQ1
MGNLFENCTHRYSFEYIYENCTNTTNQCGLIRNVASSIDVFHWLDVYISTTIFVISGILNFYCLFIALYT
YYFLDNETRKHYVFVLSRFLSSILVIISLLVLESTLFSESLSPTFAYYAVAFSIYDFSMDTLFFSYIMIS
LITYFGVVHYNFYRRHVSLRSLYIILISMWTFSLAIAIPLGLYEAASNSQGPIKCDLSYCGKVVEWITCS
LQGCDSFYNANELLVQSIISSVETLVGSLVFLTDPLINIFFDKNISKMVKLQLTLGKWFIALYRFLFQMT
NIFENCSTHYSFEKNLQKCVNASNPCQLLQKMNTAHSLMIWMGFYIPSAMCFLAVLVDTYCLLVTISILK
SLKKQSRKQYIFGRANIIGEHNDYVVVRLSAAILIALCIIIIQSTYFIDIPFRDTFAFFAVLFIIYDFSILSLLGSFTGVA
M MTYFGVMRPLVYRDKFTLKTIYIIAFAIVLFSVCVAIPFGLFQAADEIDGPIKCDSESCELIVKWLLFCI
ACLILMGCTGTLLFVTVSLHWHSYKSKKMGNVSSSAFNHGKSRLTWTTTILVILCCVELIPTGLLAAFGK
SESISDDCYDFYNANSLIFPAIVSSLETFLGSITFLLDPIINFSFDKRISKVFSSQVSMFSIFFCGKR
>SEQ2
MLDDRARMEA AKKEKVEQIL AEFQLQEEDL KKVMRRMQKE MDRGLRLETH EEASVKMLPT YVRSTPEGSE
VGDFLSLDLG GTNFRVMLVK VGEGEEGQWS VKTKHQMYSI PEDAMTGTAE MLFDYISECI SDFLDKHQMK
HKKLPLGFTF SFPVRHEDID KGILLNWTKG FKASGAEGNN VVGLLRDAIK RRGDFEMDVV AMVNDTVATM
ISCYYEDHQC EVGMIVGTGC NACYMEEMQN VELVEGDEGR MCVNTEWGAF GDSGELDEFL LEYDRLVDES
SANPGQQLYE KLIGGKYMGE LVRLVLLRLV DENLLFHGEA SEQLRTRGAF ETRFVSQVES DTGDRKQIYN
ILSTLGLRPS TTDCDIVRRA CESVSTRAAH MCSAGLAGVI NRMRESRSED VMRITVGVDG SVYKLHPSFK
ERFHASVRRL TPSCEITFIE SEEGSGRGAA LVSAVACKKA CMLGQ
>SEQ3
MESDSFEDFLKGEDFSNYSYSSDLPPFLLDAAPCEPESLEINKYFVVIIYVLVFLLSLLGNSLVMLVILY
SRVGRSGRDNVIGDHVDYVTDVYLLNLALADLLFALTLPIWAASKVTGWIFGTFLCKVVSLLKEVNFYSGILLLA
CISVDRY
LAIVHATRTLTQKRYLVKFICLSIWGLSLLLALPVLIFRKTIYPPYVSPVCYEDMGNNTANWRMLLRILP
QSFGFIVPLLIMLFCYGFTLRTLFKAHMGQKHRAMRVIFAVVLIFLLCWLPYNLVLLADTLMRTWVIQET
CERRNDIDRALEATEILGILGRVNLIGEHWDYHSCLNPLIYAFIGQKFRHGLLKILAIHGLISKDSLPKDSRPSFVGS
SSGH TSTTL
>SEQ4
MEANFQQAVK KLVNDFEYPT ESLREAVKEF DELRQKGLQK NGEVLAMAPA FISTLPTGAE TGDFLALDFG
GTNLRVCWIQ LLGDGKYEMK HSKSVLPREC VRNESVKPII DFMSDHVELF IKEHFPSKFG CPEEEYLPMG
FTFSYPANQV SITESYLLRW TKGLNIPEAI NKDFAQFLTE GFKARNLPIR IEAVINDTVG TLVTRAYTSK
ESDTFMGIIF GTGTNGAYVE QMNQIPKLAG KCTGDHMLIN MEWGATDFSC LHSTRYDLLL DHDTPNAGRQ
IFEKRVGGMY LGELFRRALF HLIKVYNFNE GIFPPSITDA WSLETSVLSR MMVERSAENV RNVLSTFKFR
FRSDEEALYL WDAAHAIGRR AARMSAVPIA SLYLSTGRAG KKSDVGVDGS LVEHYPHFVD MLREALRELI
GDNEKLISIG IAKDGSGIGA ALCALQAVKE KKGLA MEANFQQAVK KLVNDFEYPT ESLREAVKEF
DELRQKGLQK NGEVLAMAPA FISTLPTGAE TGDFLALDFG GTNLRVCWIQ LLGDGKYEMK HSKSVLPREC
VRNESVKPII DFMSDHVELF IKEHFPSKFG CPEEEYLPMG FTFSYPANQV SITESYLLRW TKGLNIPEAI
NKDFAQFLTE GFKARNLPIR IEAVINDTVG TLVTRAYTSK ESDTFMGIIF GTGTNGAYVE QMNQIPKLAG
KCTGDHMLIN MEWGATDFSC LHSTRYDLLL DHDTPNAGRQ IFEKRVGGMY LGELFRRALF HLIKVYNFNE
GIFPPSITDA WSLETSVLSR MMVERSAENV RNVLSTFKFR FRSDEEALYL WDAAHAIGRR AARMSAVPIA
SLYLSTGRAG KKSDVGVDGS LVEHYPHFVD MLREALRELI GDNEKLISIG IAKDGSGIGA ALCALQAVKE
KKGLA
sequences