💻 Б6: Пронаоѓање на сите CDS¶

Опис на барање

Со помош на BioPython, пронајдете ги секвенциите на различните кодни региони означени како (CDS). CDS се регионите добиени после процедурата на отсекување на интроните.

from Bio import SeqIO
gene_record = SeqIO.read("yersinia-pestis-fasta/NC_005816.gb", "genbank")

Вкупната должина на ДНА секвенцата е:

print(len(gene_record.seq))

Додека нас не интересира елементот од gene_record.features, кој е листа од карактеристики од големо значење за описот на самата секвенца. Откако ќе се започне со користење на овие секвенци, ова е еден вид на организација што лесно ни озвозможува да добиеме “поапстрактна” информација што се знае за самата секвенца.

Вкупниот број на овие features може да го добиеме со:

print(len(gene_record.features))

Секој еден feature има неколку атрибути, како на пример првиот од листата гледаме дека има повеќе променливи кои го опишваат меѓу кои најбитни се:

.type: типот на карактеристика (“CDS”, “gene”, …)
.location: локација на самата секвенца, како вид мапирање (почеток:крај)

dir(gene_record.features[0])

['__bool__',
 '__class__',
 '__contains__',
 '__delattr__',
 '__dict__',
 '__dir__',
 '__doc__',
 '__eq__',
 '__format__',
 '__ge__',
 '__getattribute__',
 '__gt__',
 '__hash__',
 '__init__',
 '__init_subclass__',
 '__iter__',
 '__le__',
 '__len__',
 '__lt__',
 '__module__',
 '__ne__',
 '__new__',
 '__reduce__',
 '__reduce_ex__',
 '__repr__',
 '__setattr__',
 '__sizeof__',
 '__str__',
 '__subclasshook__',
 '__weakref__',
 '_flip',
 '_get_location_operator',
 '_get_ref',
 '_get_ref_db',
 '_get_strand',
 '_set_location_operator',
 '_set_ref',
 '_set_ref_db',
 '_set_strand',
 '_shift',
 'extract',
 'id',
 'location',
 'location_operator',
 'qualifiers',
 'ref',
 'ref_db',
 'strand',
 'translate',
 'type']

Пример од книгата, и интересен CDS е “pim” генот, YP_pPCP05 кој се наоѓа во секвенцата меѓу базните парови [4342:4780]:

print(gene_record.features[21])

type: CDS
location: [4342:4780](+)
qualifiers:
    Key: codon_start, Value: ['1']
    Key: db_xref, Value: ['GI:45478716', 'GeneID:2767712']
    Key: gene, Value: ['pim']
    Key: locus_tag, Value: ['YP_pPCP05']
    Key: note, Value: ['similar to many previously sequenced pesticin immunity protein entries of Yersinia pestis plasmid pPCP, e.g. gi| 16082683|,ref|NP_395230.1| (NC_003132) , gi|1200166|emb|CAA90861.1| (Z54145 ) , gi|1488655| emb|CAA63439.1| (X92856) , gi|2996219|gb|AAC62543.1| (AF053945) , and gi|5763814|emb|CAB531 67.1| (AL109969)']
    Key: product, Value: ['pesticin immunity protein']
    Key: protein_id, Value: ['NP_995571.1']
    Key: transl_table, Value: ['11']
    Key: translation, Value: ['MGGGMISKLFCLALIFLSSSGLAEKNTYTAKDILQNLELNTFGNSLSHGIYGKQTTFKQTEFTNIKSNTKKHIALINKDNSWMISLKILGIKRDEYTVCFEDFSLIRPPTYVAIHPLLIKKVKSGNFIVVKEIKKSIPGCTVYYH']

Но, ние треба да ги најдее сите вакви CDS кодони и ова може да го направиме со тоа што ќе бараме низ целата низа од 41 features каде се наоѓаат оние кои имаат тип “CDS”:

CDS_list = []

for i in range(0, len(gene_record.features)):
    if gene_record.features[i].type == "CDS":
        CDS_list.append(i)

print(f"Број на пронајдени CDS: {len(CDS_list)}")

Број на пронајдени CDS: 10

Вакви гледаме дека се вкупно 10, и нив можеме да ги испринтаме:

for i in CDS_list:
    print(gene_record.features[i])

type: CDS
location: [86:1109](+)
qualifiers:
    Key: codon_start, Value: ['1']
    Key: db_xref, Value: ['GI:45478712', 'GeneID:2767718']
    Key: locus_tag, Value: ['YP_pPCP01']
    Key: note, Value: ['similar to corresponding CDS from previously sequenced pPCP plasmid of Yersinia pestis KIM (AF053945) and CO92 (AL109969), also many transposase entries for insertion sequence IS100 of Yersinia pestis. Contains IS21-like element transposase, HTH domain (Interpro|IPR007101)']
    Key: product, Value: ['putative transposase']
    Key: protein_id, Value: ['NP_995567.1']
    Key: transl_table, Value: ['11']
    Key: translation, Value: ['MVTFETVMEIKILHKQGMSSRAIARELGISRNTVKRYLQAKSEPPKYTPRPAVASLLDEYRDYIRQRIADAHPYKIPATVIAREIRDQGYRGGMTILRAFIRSLSVPQEQEPAVRFETEPGRQMQVDWGTMRNGRSPLHVFVAVLGYSRMLYIEFTDNMRYDTLETCHRNAFRFFGGVPREVLYDNMKTVVLQRDAYQTGQHRFHPSLWQFGKEMGFSPRLCRPFRAQTKGKVERMVQYTRNSFYIPLMTRLRPMGITVDVETANRHGLRWLHDVANQRKHETIQARPCDRWLEEQQSMLALPPEKKEYDVHLDENLVNFDKHPLHHPLSIYDSFCRGVA']

type: CDS
location: [1105:1888](+)
qualifiers:
    Key: codon_start, Value: ['1']
    Key: db_xref, Value: ['GI:45478713', 'GeneID:2767716']
    Key: locus_tag, Value: ['YP_pPCP02']
    Key: note, Value: ['similar to corresponding CDS form previously sequenced pPCP plasmid of Yersinia pestis KIM (AF053945) and CO92 (AL109969), also many ATP-binding protein entries for insertion sequence IS100 of Yersinia pestis. Contains Chaperonin clpA/B (Interpro|IPR001270). Contains ATP/GTP-binding site motif A (P-loop) (Interpro|IPR001687, Molecular Function: ATP binding (GO:0005524)). Contains Bacterial chromosomal replication initiator protein, DnaA (Interpro|IPR001957, Molecular Function: DNA binding (GO:0003677), Molecular Function: DNA replication origin binding (GO:0003688), Molecular Function: ATP binding (GO:0005524), Biological Process: DNA replication initiation (GO:0006270), Biological Process: regulation of DNA replication (GO:0006275)). Contains AAA ATPase (Interpro|IPR003593, Molecular Function: nucleotide binding (GO:0000166))']
    Key: product, Value: ['transposase/IS protein']
    Key: protein_id, Value: ['NP_995568.1']
    Key: transl_table, Value: ['11']
    Key: translation, Value: ['MMMELQHQRLMALAGQLQLESLISAAPALSQQAVDQEWSYMDFLEHLLHEEKLARHQRKQAMYTRMAAFPAVKTFEEYDFTFATGAPQKQLQSLRSLSFIERNENIVLLGPSGVGKTHLAIAMGYEAVRAGIKVRFTTAADLLLQLSTAQRQGRYKTTLQRGVMAPRLLIIDEIGYLPFSQEEAKLFFQVIAKRYEKSAMILTSNLPFGQWDQTFAGDAALTSAMLDRILHHSHVVQIKGESYRLRQKRKAGVIAEANPE']

type: CDS
location: [2924:3119](+)
qualifiers:
    Key: codon_start, Value: ['1']
    Key: db_xref, Value: ['GI:45478714', 'GeneID:2767717']
    Key: gene, Value: ['rop']
    Key: gene_synonym, Value: ['rom']
    Key: locus_tag, Value: ['YP_pPCP03']
    Key: note, Value: ['Best Blastp hit =gi|16082682|ref|NP_395229.1| (NC_003132) putative replication regulatory protein [Yersinia pestis], gi|5763813|emb|CAB531 66.1| (AL109969) putative replication regulatory protein [Yersinia pestis]; similar to gb|AAK91579.1| (AY048853), RNAI modulator protein Rom [Salmonella choleraesuis], Contains Regulatory protein Rop (Interpro|IPR000769)']
    Key: product, Value: ['putative replication regulatory protein']
    Key: protein_id, Value: ['NP_995569.1']
    Key: transl_table, Value: ['11']
    Key: translation, Value: ['MNKQQQTALNMARFIRSQSLILLEKLDALDADEQAAMCERLHELAEELQNSIQARFEAESETGT']

type: CDS
location: [3485:3857](+)
qualifiers:
    Key: codon_start, Value: ['1']
    Key: db_xref, Value: ['GI:45478715', 'GeneID:2767720']
    Key: locus_tag, Value: ['YP_pPCP04']
    Key: note, Value: ['Best Blastp hit = gi|321919|pir||JQ1541 hypothetical 16.9K protein - Salmonella typhi murium plasmid NTP16.']
    Key: product, Value: ['hypothetical protein']
    Key: protein_id, Value: ['NP_995570.1']
    Key: transl_table, Value: ['11']
    Key: translation, Value: ['MSKKRRPQKRPRRRRFFHRLRPPDEHHKNRRSSQRWRNPTGLKDTRRFPPEAPSCALLFRPCRLPDTSPPFSLREAWRFLIAHAVGISVRCRSFAPSWAVCTNPPFSPTTAPYPVTIVLSPTR']

type: CDS
location: [4342:4780](+)
qualifiers:
    Key: codon_start, Value: ['1']
    Key: db_xref, Value: ['GI:45478716', 'GeneID:2767712']
    Key: gene, Value: ['pim']
    Key: locus_tag, Value: ['YP_pPCP05']
    Key: note, Value: ['similar to many previously sequenced pesticin immunity protein entries of Yersinia pestis plasmid pPCP, e.g. gi| 16082683|,ref|NP_395230.1| (NC_003132) , gi|1200166|emb|CAA90861.1| (Z54145 ) , gi|1488655| emb|CAA63439.1| (X92856) , gi|2996219|gb|AAC62543.1| (AF053945) , and gi|5763814|emb|CAB531 67.1| (AL109969)']
    Key: product, Value: ['pesticin immunity protein']
    Key: protein_id, Value: ['NP_995571.1']
    Key: transl_table, Value: ['11']
    Key: translation, Value: ['MGGGMISKLFCLALIFLSSSGLAEKNTYTAKDILQNLELNTFGNSLSHGIYGKQTTFKQTEFTNIKSNTKKHIALINKDNSWMISLKILGIKRDEYTVCFEDFSLIRPPTYVAIHPLLIKKVKSGNFIVVKEIKKSIPGCTVYYH']

type: CDS
location: [4814:5888](-)
qualifiers:
    Key: codon_start, Value: ['1']
    Key: db_xref, Value: ['GI:45478717', 'GeneID:2767721']
    Key: gene, Value: ['pst']
    Key: locus_tag, Value: ['YP_pPCP06']
    Key: note, Value: ['Best Blastp hit =|16082684|ref|NP_395231.1| (NC_003132) pesticin [Yersinia pestis], gi|984824|gb|AAA75369.1| (U31974) pesticin [Yersinia pestis], gi|1488654|emb|CAA63438.1| (X92856) pesticin [Yersinia pestis], gi|2996220|gb|AAC62544.1| (AF053945) pesticin [Yersinia pestis], gi|5763815|emb|CAB53168.1| (AL1099 69) pesticin [Yersinia pestis]']
    Key: product, Value: ['pesticin']
    Key: protein_id, Value: ['NP_995572.1']
    Key: transl_table, Value: ['11']
    Key: translation, Value: ['MSDTMVVNGSGGVPAFLFSGSTLSSYRPNFEANSITIALPHYVDLPGRSNFKLMYIMGFPIDTEMEKDSEYSNKIRQESKISKTEGTVSYEQKITVETGQEKDGVKVYRVMVLEGTIAESIEHLDKKENEDILNNNRNRIVLADNTVINFDNISQLKEFLRRSVNIVDHDIFSSNGFEGFNPTSHFPSNPSSDYFNSTGVTFGSGVDLGQRSKQDLLNDGVPQYIADRLDGYYMLRGKEAYDKVRTAPLTLSDNEAHLLSNIYIDKFSHKIEGLFNDANIGLRFSDLPLRTRTALVSIGYQKGFKLSRTAPTVWNKVIAKDWNGLVNAFNNIVDGMSDRRKREGALVQKDIDSGLLK']

type: CDS
location: [6004:6421](+)
qualifiers:
    Key: codon_start, Value: ['1']
    Key: db_xref, Value: ['GI:45478718', 'GeneID:2767719']
    Key: locus_tag, Value: ['YP_pPCP07']
    Key: note, Value: ['Best Blastp hit = gi|16082685|ref|NP_395232.1| (NC_003132) hypothetical protein [Yersinia pestis], gi|5763816|emb|CAB53169.1| (AL109969) hypothetical protein [Yersinia pestis]']
    Key: product, Value: ['hypothetical protein']
    Key: protein_id, Value: ['NP_995573.1']
    Key: transl_table, Value: ['11']
    Key: translation, Value: ['MKFHFCDLNHSYKNQEGKIRSRKTAPGNIRKKQKGDNVSKTKSGRHRLSKTDKRLLAALVVAGYEERTARDLIQKHVYTLTQADLRHLVSEISNGVGQSQAYDAIYQARRIRLARKYLSGKKPEGVEPREGQEREDLP']

type: CDS
location: [6663:7602](+)
qualifiers:
    Key: EC_number, Value: ['3.4.23.48']
    Key: codon_start, Value: ['1']
    Key: db_xref, Value: ['GI:45478719', 'GeneID:2767715']
    Key: gene, Value: ['pla']
    Key: locus_tag, Value: ['YP_pPCP08']
    Key: note, Value: ['outer membrane protease; involved in virulence in many organisms; OmpT; IcsP; SopA; Pla; PgtE; omptin; in Escherichia coli OmpT can degrade antimicrobial peptides; in Yersinia Pla activates plasminogen during infection; in Shigella flexneria SopA cleaves the autotransporter IcsA']
    Key: product, Value: ['outer membrane protease']
    Key: protein_id, Value: ['NP_995574.1']
    Key: transl_table, Value: ['11']
    Key: translation, Value: ['MKKSSIVATIITILSGSANAASSQLIPNISPDSFTVAASTGMLSGKSHEMLYDAETGRKISQLDWKIKNVAILKGDISWDPYSFLTLNARGWTSLASGSGNMDDYDWMNENQSEWTDHSSHPATNVNHANEYDLNVKGWLLQDENYKAGITAGYQETRFSWTATGGSYSYNNGAYTGNFPKGVRVIGYNQRFSMPYIGLAGQYRINDFELNALFKFSDWVRAHDNDEHYMRDLTFREKTSGSRYYGTVINAGYYVTPNAKVFAEFTYSKYDEGKGGTQIIDKNSGDSVSIGGDAAGISNKNYTVTAGLQYRF']

type: CDS
location: [7788:8088](-)
qualifiers:
    Key: codon_start, Value: ['1']
    Key: db_xref, Value: ['GI:45478720', 'GeneID:2767713']
    Key: locus_tag, Value: ['YP_pPCP09']
    Key: note, Value: ['Best Blastp hit = gi|16082687|ref|NP_395234.1| (NC_003132) putative transcriptional regulator [Yersinia pestis], gi|5763818|emb|CAB53171.1| (AL109969) putative transcriptional regulator [Yersinia pestis].']
    Key: product, Value: ['putative transcriptional regulator']
    Key: protein_id, Value: ['NP_995575.1']
    Key: transl_table, Value: ['11']
    Key: translation, Value: ['MRTLDEVIASRSPESQTRIKEMADEMILEVGLQMMREELQLSQKQVAEAMGISQPAVTKLEQRGNDLKLATLKRYVEAMGGKLSLDVELPTGRRVAFHV']

type: CDS
location: [8087:8360](-)
qualifiers:
    Key: codon_start, Value: ['1']
    Key: db_xref, Value: ['GI:45478721', 'GeneID:2767714']
    Key: locus_tag, Value: ['YP_pPCP10']
    Key: note, Value: ['Best Blastp hit = gi|16082688|ref|NP_395235.1| (NC_003132) hypothetical protein [ Yersinia pestis], gi|5763819|emb|CAB53172.1| (AL109969) hypothetical protein [Yersinia pestis]']
    Key: product, Value: ['hypothetical protein']
    Key: protein_id, Value: ['NP_995576.1']
    Key: transl_table, Value: ['11']
    Key: translation, Value: ['MADLKKLQVYGPELPRPYADTVKGSRYKNMKELRVQFSGRPIRAFYAFDPIRRAIVLCAGDKSNDKRFYEKLVRIAEDEFTAHLNTLESK']

Лабораториска вежба Биоинформатика

💻 Б6: Пронаоѓање на сите CDS¶