Harvard:Biophysics 101/2007/Notebook:HRH/2007-2-6
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Script:
#!/usr/bin/env python
# Hetmann Hsieh
# Assignment 1
# 2/6/07
from Bio import GenBank, Seq
# We can create a GenBank object that will parse a raw record
# This facilitates extracting specific information from the sequences
record_parser = GenBank.FeatureParser()
# NCBIDictionary is an interface to Genbank
ncbi_dict = GenBank.NCBIDictionary('nucleotide', 'genbank', parser = record_parser)
# If you pass NCBIDictionary a GenBank id, it will download that record
parsed_record = ncbi_dict['116496644']
print "GenBank id:", parsed_record.id
# Extract the sequence from the parsed_record
s = parsed_record.seq.tostring()
print "total sequence length:", len(s)
max_repeat = 9
print "method 1"
for i in range(max_repeat):
substr = ''.join(['T' for n in range(i+1)])
print substr, s.count(substr)
print "\nmethod 2"
for i in range(max_repeat):
substr = ''.join(['T' for n in range(i+1)])
count = 0
pos = s.find(substr,0)
while not pos == -1:
count = count + 1
pos = s.find(substr,pos+1)
print substr, count
# Other parts of the assignment are as follows
# Print the translated protein sequence and length
from Bio.Seq import translate
print "protein translation:"
protein = translate(s)
print protein
print "protein length:", len(protein)
# New NCBIDictionary without a parser, printing of raw record
ncbi_dict2 = GenBank.NCBIDictionary('nucleotide', 'genbank')
raw_record = ncbi_dict2['116496644']
print raw_record
Output:
GenBank id: BC126205.1
total sequence length: 3773
method 1
T 805
TT 115
TTT 28
TTTT 3
TTTTT 0
TTTTTT 0
TTTTTTT 0
TTTTTTTT 0
TTTTTTTTT 0
method 2
T 805
TT 143
TTT 31
TTTT 3
TTTTT 0
TTTTTT 0
TTTTTTT 0
TTTTTTTT 0
TTTTTTTTT 0
protein translation:
EGERLKEAMRSPRTRGRSGRPLSLLLALLCALRAKVCGASGQFELEILSMQNVNGELQNGNCCGGARNPGDRKCTRDECDTYFKVCLKEYQSRVTAGGPCSFGSGSTPVIGGNTFNLKASRGNDRNRIVLPFSFAWPRSYTLLVEAWDSSNDTVQPDSIIEKASHSGMINPSRQWQTLKQNTGVAHFEYQIRVTCDDYYYGFGCNKFCRPRDDFFGHYACDQNGNKTCMEGWMGPECNRAICRQGCSPKHGSCKLPGDCRCQYGWQGLYCDKCIPHPGCVHGICNEPWQCLCETNWGGQLCDKDLNYCGTHQPCLNGGTCSNTGPDKYQCSCPEGYSGPNCEIAEHACLSDPCHNRGSCKETSLGFECECSPGWTGPTCSTNIDDCSPNNCSHGGTCQDLVNGFKCVCPPQWTGKTCQLDANECEAKPCVNAKSCKNLIASYYCDCLPGWMGQNCDININDCLGQCQNDASCRDLVNGYRCICPPGYAGDHCERDIDECASNPCLNGGHCQNEINRFQCLCPTGFSGNLCQLDIDYCEPNPCQNGAQCYNRASDYFCKCPEDYEGKNCSHLKDHCRTTPCEVIDSCTVAMASNDTPEGVRYISSNVCGPHGKCKSQSGGKFTCDCNKGFTGTYCHENINDCESNPCRNGGTCIDGVNSYKCICSDGWEGAYCETNINDCSQNPCHNGGTCRDLVNDFYCDCKNGWKGKTCHSRDSQCDEATCNNGGTCYDEGDAFKCMCPGGWEGTTCNIARNSSCLPNPCHNGGTCVVNGESFTCVCKEGWEGPICAQNTNDCSPHPCYNSGTCVDGDNWYRCECAPGFAGPDCRININECQSSPCAFGATCVDEINGYRCVCPPGHSGAKCQEVSGRPCITMGSVIPDGAKWDDDCNTCQCLNGRIACSKVWCGPRPCLLHKGHSECPSGQSCIPILDDQCFVHPCTGVGECRSSSLQPVKTKCTSDSYYQDNCANITFTFNKEMMSPGLTTEHICSELRNLNILKNVSAEYSIYIACEPSPSANNEIHVAISAEDIRDDGNPIKEITDKIIDLVSKRDGNSSLIAAVAEVRVQRRPLKNRTDFLVPLLSSVLTVAWICCLVTAFYWCLRKRRKPGSHTHSASEDNTTNNVREQLNQIKNPIEKHGANTVPIKDYENKNSKMSKIRTHNSEVEEDDMDKHQQKARFAKQPAYTLVDREEKPPNGTPTKHPNWTNKQDNRDLESAQSLNRMEYIV*QTAGTAAAR*SLRACSSLNCRVILESEAVA
protein length: 1257
LOCUS BC126205 3773 bp mRNA linear PRI 23-OCT-2006
DEFINITION Homo sapiens jagged 1 (Alagille syndrome), mRNA (cDNA clone
MGC:161483 IMAGE:8991921), complete cds.
ACCESSION BC126205
VERSION BC126205.1 GI:116496644
KEYWORDS MGC.
SOURCE Homo sapiens (human)
ORGANISM Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
REFERENCE 1 (bases 1 to 3773)
AUTHORS Strausberg,R.L., Feingold,E.A., Grouse,L.H., Derge,J.G.,
Klausner,R.D., Collins,F.S., Wagner,L., Shenmen,C.M., Schuler,G.D.,
Altschul,S.F., Zeeberg,B., Buetow,K.H., Schaefer,C.F., Bhat,N.K.,
Hopkins,R.F., Jordan,H., Moore,T., Max,S.I., Wang,J., Hsieh,F.,
Diatchenko,L., Marusina,K., Farmer,A.A., Rubin,G.M., Hong,L.,
Stapleton,M., Soares,M.B., Bonaldo,M.F., Casavant,T.L.,
Scheetz,T.E., Brownstein,M.J., Usdin,T.B., Toshiyuki,S.,
Carninci,P., Prange,C., Raha,S.S., Loquellano,N.A., Peters,G.J.,
Abramson,R.D., Mullahy,S.J., Bosak,S.A., McEwan,P.J.,
McKernan,K.J., Malek,J.A., Gunaratne,P.H., Richards,S.,
Worley,K.C., Hale,S., Garcia,A.M., Gay,L.J., Hulyk,S.W.,
Villalon,D.K., Muzny,D.M., Sodergren,E.J., Lu,X., Gibbs,R.A.,
Fahey,J., Helton,E., Ketteman,M., Madan,A., Rodrigues,S.,
Sanchez,A., Whiting,M., Madan,A., Young,A.C., Shevchenko,Y.,
Bouffard,G.G., Blakesley,R.W., Touchman,J.W., Green,E.D.,
Dickson,M.C., Rodriguez,A.C., Grimwood,J., Schmutz,J., Myers,R.M.,
Butterfield,Y.S., Krzywinski,M.I., Skalska,U., Smailus,D.E.,
Schnerch,A., Schein,J.E., Jones,S.J. and Marra,M.A.
CONSRTM Mammalian Gene Collection Program Team
TITLE Generation and initial analysis of more than 15,000 full-length
human and mouse cDNA sequences
JOURNAL Proc. Natl. Acad. Sci. U.S.A. 99 (26), 16899-16903 (2002)
PUBMED 12477932
REFERENCE 2 (bases 1 to 3773)
CONSRTM NIH MGC Project
TITLE Direct Submission
JOURNAL Submitted (22-OCT-2006) National Institutes of Health, Mammalian
Gene Collection (MGC), Bethesda, MD 20892-2590, USA
REMARK NIH-MGC Project URL: http://mgc.nci.nih.gov
COMMENT Contact: MGC help desk
Email: cgapbs-r@mail.nih.gov
Tissue Procurement: Mike Brownstein, NIMH
cDNA Library Preparation: British Columbia Cancer Research Center
cDNA Library Arrayed by: The I.M.A.G.E. Consortium (LLNL)
DNA Sequencing by: Genome Sequence Centre,
BC Cancer Agency, Vancouver, BC, Canada
info@bcgsc.bc.ca
Martin Hirst, Thomas Zeng, Ryan Morin, Michelle Moksa, Johnson
Pang, Diana Mah, Jing Wang, Kieth Fichter, Eric Chuah, Allen
Delaney, Rob Kirkpatrick, Agnes Baross, Sarah Barber, Mabel
Brown-John, Steve S. Chand, William Chow, Ryan Babakaiff, Dave
Wong, Corey Matsuo, Jaclyn Beland, Susan Gibson, Luis delRio, Ruth
Featherstone, Malachi Griffith, Obi Griffith, Ran Guin, Nancy Liao,
Kim MacDonald, Mike R. Mayo, Josh Moran, Diana Palmquist, JR
Santos, Duane Smailus, Jeff Stott, Miranda Tsai, George Yang,
Jacquie Schein, Asim Siddiqui,Steven Jones, Rob Holt, Marco Marra.
Clone distribution: MGC clone distribution information can be found
through the I.M.A.G.E. Consortium/LLNL at: http://image.llnl.gov
Series: IRCB Plate: 7 Row: E Column: 7.
Differences found between this sequence and the human reference
genome (build 36) are described in misc_difference features below
and these differences were also compared to chimpanzee genome
(build 2).
FEATURES Location/Qualifiers
source 1..3773
/organism="Homo sapiens"
/mol_type="mRNA"
/db_xref="taxon:9606"
/clone="MGC:161483 IMAGE:8991921"
/tissue_type="Brain, cerebellum, PCR rescued clones"
/clone_lib="NIH_MGC_313"
/note="Vector: pCR-XL-TOPO with reversed insert; Clone
identification sequence tag: GACACATT"
gene 1..3773
/gene="JAG1"
/note="synonyms: AWS, HJ1, AHD, CD339"
/db_xref="GeneID:182"
/db_xref="HGNC:6188"
/db_xref="MIM:601920"
CDS 25..3681
/gene="JAG1"
/codon_start=1
/product="jagged 1 (Alagille syndrome)"
/protein_id="AAI26206.1"
/db_xref="GI:116496645"
/db_xref="GeneID:182"
/db_xref="HGNC:6188"
/db_xref="MIM:601920"
/translation="MRSPRTRGRSGRPLSLLLALLCALRAKVCGASGQFELEILSMQN
VNGELQNGNCCGGARNPGDRKCTRDECDTYFKVCLKEYQSRVTAGGPCSFGSGSTPVI
GGNTFNLKASRGNDRNRIVLPFSFAWPRSYTLLVEAWDSSNDTVQPDSIIEKASHSGM
INPSRQWQTLKQNTGVAHFEYQIRVTCDDYYYGFGCNKFCRPRDDFFGHYACDQNGNK
TCMEGWMGPECNRAICRQGCSPKHGSCKLPGDCRCQYGWQGLYCDKCIPHPGCVHGIC
NEPWQCLCETNWGGQLCDKDLNYCGTHQPCLNGGTCSNTGPDKYQCSCPEGYSGPNCE
IAEHACLSDPCHNRGSCKETSLGFECECSPGWTGPTCSTNIDDCSPNNCSHGGTCQDL
VNGFKCVCPPQWTGKTCQLDANECEAKPCVNAKSCKNLIASYYCDCLPGWMGQNCDIN
INDCLGQCQNDASCRDLVNGYRCICPPGYAGDHCERDIDECASNPCLNGGHCQNEINR
FQCLCPTGFSGNLCQLDIDYCEPNPCQNGAQCYNRASDYFCKCPEDYEGKNCSHLKDH
CRTTPCEVIDSCTVAMASNDTPEGVRYISSNVCGPHGKCKSQSGGKFTCDCNKGFTGT
YCHENINDCESNPCRNGGTCIDGVNSYKCICSDGWEGAYCETNINDCSQNPCHNGGTC
RDLVNDFYCDCKNGWKGKTCHSRDSQCDEATCNNGGTCYDEGDAFKCMCPGGWEGTTC
NIARNSSCLPNPCHNGGTCVVNGESFTCVCKEGWEGPICAQNTNDCSPHPCYNSGTCV
DGDNWYRCECAPGFAGPDCRININECQSSPCAFGATCVDEINGYRCVCPPGHSGAKCQ
EVSGRPCITMGSVIPDGAKWDDDCNTCQCLNGRIACSKVWCGPRPCLLHKGHSECPSG
QSCIPILDDQCFVHPCTGVGECRSSSLQPVKTKCTSDSYYQDNCANITFTFNKEMMSP
GLTTEHICSELRNLNILKNVSAEYSIYIACEPSPSANNEIHVAISAEDIRDDGNPIKE
ITDKIIDLVSKRDGNSSLIAAVAEVRVQRRPLKNRTDFLVPLLSSVLTVAWICCLVTA
FYWCLRKRRKPGSHTHSASEDNTTNNVREQLNQIKNPIEKHGANTVPIKDYENKNSKM
SKIRTHNSEVEEDDMDKHQQKARFAKQPAYTLVDREEKPPNGTPTKHPNWTNKQDNRD
LESAQSLNRMEYIV"
misc_difference 789
/gene="JAG1"
/note="'T' in cDNA is 'C' in the human genome; no amino
acid change. The chimpanzee genome agrees with the human
genomic sequence and not the cDNA."
misc_difference 3441
/gene="JAG1"
/note="'C' in cDNA is 'T' in the human genome; no amino
acid change."
ORIGIN
1 gagggggagc gtctcaaaga agcgatgcgt tccccacgga cgcgcggccg gtccgggcgc
61 cccctaagcc tcctgctcgc cctgctctgt gccctgcgag ccaaggtgtg tggggcctcg
121 ggtcagttcg agttggagat cctgtccatg cagaacgtga acggggagct gcagaacggg
181 aactgctgcg gcggcgcccg gaacccggga gaccgcaagt gcacccgcga cgagtgtgac
241 acatacttca aagtgtgcct caaggagtat cagtcccgcg tcacggccgg ggggccctgc
301 agcttcggct cagggtccac gcctgtcatc gggggcaaca ccttcaacct caaggccagc
361 cgcggcaacg accgcaaccg catcgtgctg cctttcagtt tcgcctggcc gaggtcctat
421 acgttgcttg tggaggcgtg ggattccagt aatgacaccg ttcaacctga cagtattatt
481 gaaaaggctt ctcactcggg catgatcaac cccagccggc agtggcagac gctgaagcag
541 aacacgggcg ttgcccactt tgagtatcag atccgcgtga cctgtgatga ctactactat
601 ggctttggct gcaataagtt ctgccgcccc agagatgact tctttggaca ctatgcctgt
661 gaccagaatg gcaacaaaac ttgcatggaa ggctggatgg gccccgaatg taacagagct
721 atttgccgac aaggctgcag tcctaagcat gggtcttgca aactcccagg tgactgcagg
781 tgccagtatg gctggcaagg cctgtactgt gataagtgca tcccacaccc gggatgcgtc
841 cacggcatct gtaatgagcc ctggcagtgc ctctgtgaga ccaactgggg cggccagctc
901 tgtgacaaag atctcaatta ctgtgggact catcagccgt gtctcaacgg gggaacttgt
961 agcaacacag gccctgacaa atatcagtgt tcctgccctg aggggtattc aggacccaac
1021 tgtgaaattg ctgagcacgc ctgcctctct gatccctgtc acaacagagg cagctgtaag
1081 gagacctccc tgggctttga gtgtgagtgt tccccaggct ggaccggccc cacatgctct
1141 acaaacattg atgactgttc tcctaataac tgttcccacg ggggcacctg ccaggacctg
1201 gttaacggat ttaagtgtgt gtgcccccca cagtggactg ggaaaacgtg ccagttagat
1261 gcaaatgaat gtgaggccaa accttgtgta aacgccaaat cctgtaagaa tctcattgcc
1321 agctactact gcgactgtct tcccggctgg atgggtcaga attgtgacat aaatattaat
1381 gactgccttg gccagtgtca gaatgacgcc tcctgtcggg atttggttaa tggttatcgc
1441 tgtatctgtc cacctggcta tgcaggcgat cactgtgaga gagacatcga tgaatgtgcc
1501 agcaacccct gtttgaatgg gggtcactgt cagaatgaaa tcaacagatt ccagtgtctg
1561 tgtcccactg gtttctctgg aaacctctgt cagctggaca tcgattattg tgagcctaat
1621 ccctgccaga acggtgccca gtgctacaac cgtgccagtg actatttctg caagtgcccc
1681 gaggactatg agggcaagaa ctgctcacac ctgaaagacc actgccgcac gaccccctgt
1741 gaagtgattg acagctgcac agtggccatg gcttccaacg acacacctga aggggtgcgg
1801 tatatttcct ccaacgtctg tggtcctcac gggaagtgca agagtcagtc gggaggcaaa
1861 ttcacctgtg actgtaacaa aggcttcacg ggaacatact gccatgaaaa tattaatgac
1921 tgtgagagca acccttgtag aaacggtggc acttgcatcg atggtgtcaa ctcctacaag
1981 tgcatctgta gtgacggctg ggagggggcc tactgtgaaa ccaatattaa tgactgcagc
2041 cagaacccct gccacaatgg gggcacgtgt cgcgacctgg tcaatgactt ctactgtgac
2101 tgtaaaaatg ggtggaaagg aaagacctgc cactcacgtg acagtcagtg tgatgaggcc
2161 acgtgcaaca acggtggcac ctgctatgat gagggggatg cttttaagtg catgtgtcct
2221 ggcggctggg aaggaacaac ctgtaacata gcccgaaaca gtagctgcct gcccaacccc
2281 tgccataatg ggggcacatg tgtggtcaac ggcgagtcct ttacgtgcgt ctgcaaggaa
2341 ggctgggagg ggcccatctg tgctcagaat accaatgact gcagccctca tccctgttac
2401 aacagcggca cctgtgtgga tggagacaac tggtaccggt gcgaatgtgc cccgggtttt
2461 gctgggcccg actgcagaat aaacatcaat gaatgccagt cttcaccttg tgcctttgga
2521 gcgacctgtg tggatgagat caatggctac cggtgtgtct gccctccagg gcacagtggt
2581 gccaagtgcc aggaagtttc agggagacct tgcatcacca tggggagtgt gataccagat
2641 ggggccaaat gggatgatga ctgtaatacc tgccagtgcc tgaatggacg gatcgcctgc
2701 tcaaaggtct ggtgtggccc tcgaccttgc ctgctccaca aagggcacag cgagtgcccc
2761 agcgggcaga gctgcatccc catcctggac gaccagtgct tcgtccaccc ctgcactggt
2821 gtgggcgagt gtcggtcttc cagtctccag ccggtgaaga caaagtgcac ctctgactcc
2881 tattaccagg ataactgtgc gaacatcaca tttaccttta acaaggagat gatgtcacca
2941 ggtcttacta cggagcacat ttgcagtgaa ttgaggaatt tgaatatttt gaagaatgtt
3001 tccgctgaat attcaatcta catcgcttgc gagccttccc cttcagcgaa caatgaaata
3061 catgtggcca tttctgctga agatatacgg gatgatggga acccgatcaa ggaaatcact
3121 gacaaaataa tcgatcttgt tagtaaacgt gatggaaaca gctcgctgat tgctgccgtt
3181 gcagaagtaa gagttcagag gcggcctctg aagaacagaa cagatttcct tgttcccttg
3241 ctgagctctg tcttaactgt ggcttggatc tgttgcttgg tgacggcctt ctactggtgc
3301 ctgcggaagc ggcggaagcc gggcagccac acacactcag cctctgagga caacaccacc
3361 aacaacgtgc gggagcagct gaaccagatc aaaaacccca ttgagaaaca tggggccaac
3421 acggtcccca tcaaggatta cgagaacaag aactccaaaa tgtctaaaat aaggacacac
3481 aattctgaag tagaagagga cgacatggac aaacaccagc agaaagcccg gtttgccaag
3541 cagccggcgt acacgctggt agacagagaa gagaagcccc ccaacggcac gccgacaaaa
3601 cacccaaact ggacaaacaa acaggacaac agagacttgg aaagtgccca gagcttaaac
3661 cgaatggagt acatcgtata gcagaccgcg ggcactgccg ccgctaggta gagtctgagg
3721 gcttgtagtt ctttaaactg tcgtgtcata ctcgagtctg aggccgttgc tga
