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# Seq object
from Bio.Seq import Seq
my_seq = Seq("AGTACACTGGT")
print(my_seq)
print(my_seq.complement())
print(my_seq.reverse_complement())
# important class 
# SeqRecord; Bio.SeqIO

AGTACACTGGT
TCATGTGACCA
ACCAGTGTACT

sequence parsing 序列解析

parsing sequence file formats

Pubmed for papers

extract sequence data from genbank(Aceesing NCBI’s Entrez databases)

Swiss-Prot & ExPASy(PRO)

ClustalW(mutiple squece alignment)

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# Parsing sequence file formats
# Bio.SeqIO 模块
from Bio import SeqIO
for seq_record in SeqIO.parse(r"F:\Blog\source\_posts\bioseq\res\ls_orchid.gb", "genbank"):
    print(seq_record.id)
    print(repr(seq_record.seq))
    print(len(seq_record))
Z78533.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGAGACCGTGG...CGC')
740
Z78532.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGACAACAG...GGC')
753
Z78531.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGACAGCAG...TAA')
748
Z78530.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAAACAACAT...CAT')
744
Z78529.1
Seq('ACGGCGAGCTGCCGAAGGACATTGTTGAGACAGCAGAATATACGATTGAGTGAA...AAA')
733
Z78527.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGACAGTAG...CCC')
718
Z78526.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGACAGTAG...TGT')
730
Z78525.1
Seq('TGTTGAGATAGCAGAATATACATCGAGTGAATCCGGAGGACCTGTGGTTATTCG...GCA')
704
Z78524.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATAGTAG...AGC')
740
Z78523.1
Seq('CGTAACCAGGTTTCCGTAGGTGAACCTGCGGCAGGATCATTGTTGAGACAGCAG...AAG')
709
Z78522.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGACAGCAG...GAG')
700
Z78521.1
Seq('GTAGGTGAACCTGCGGAAGGATCATTGTTGAGACAGTAGAATATATGATCGAGT...ACC')
726
Z78520.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGACAGCAG...TTT')
753
Z78519.1
Seq('ATATGATCGAGTGAATCTGGTGGACTTGTGGTTACTCAGCTCGCCATAGGCTTT...TTA')
699
Z78518.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGGAGGATCATTGTTGAGATAGTAG...TCC')
658
Z78517.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGACAGTAG...AGC')
752
Z78516.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGACAGTAT...TAA')
726
Z78515.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGCTGAGACCGTAG...AGC')
765
Z78514.1
Seq('CGTAACAAGGTTTCCGTAGGTGGACCTTCGGGAGGATCATTTTTGAAGCCCCCA...CTA')
755
Z78513.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGACCGCCA...GAG')
742
Z78512.1
Seq('CGTAACAAGGTTTCCGTAGGTGGACCTTCGGGAGGATCATTTTTGAAGCCCCCA...AGC')
762
Z78511.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTTCGGAAGGATCATTGTTGAGACCCCCA...GGA')
745
Z78510.1
Seq('CTAACCAGGGTTCCGAGGTGACCTTCGGGAGGATTCCTTTTTAAGCCCCCGAAA...TTA')
750
Z78509.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGACCGCCA...GGA')
731
Z78508.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGACCGCCA...TGA')
741
Z78507.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGACCCCCA...TGA')
740
Z78506.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGACCGCAA...TGA')
727
Z78505.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGACCGCCA...TTT')
711
Z78504.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTTCGGAAGGATCATTGTTGAGACCGCAA...TAA')
743
Z78503.1
Seq('CGTAACCAGGTTTCCGTAGGTGAACCTCCGGAAGGATCCTTGTTGAGACCGCCA...TAA')
727
Z78502.1
Seq('CGTAACCAGGTTTCCGTAGGTGAACCTCCGGAAGGATCATTGTTGAGACCGCCA...CGC')
757
Z78501.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGACCGCAA...AGA')
770
Z78500.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGCTCATTGTTGAGACCGCAA...AAG')
767
Z78499.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAGGGATCATTGTTGAGATCGCAT...ACC')
759
Z78498.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAAGGTCATTGTTGAGATCACAT...AGC')
750
Z78497.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...AGC')
788
Z78496.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCGCAT...AGC')
774
Z78495.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTCCGGAAGGATCATTGTTGAGATCACAT...GTG')
789
Z78494.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGGTCGCAT...AAG')
688
Z78493.1
Seq('CGTAACAAGGATTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCGCAT...CCC')
719
Z78492.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCGCAT...ATA')
743
Z78491.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCGCAT...AGC')
737
Z78490.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...TGA')
728
Z78489.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...GGC')
740
Z78488.1
Seq('CTGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACGCAATAATTGATCGA...GCT')
696
Z78487.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...TAA')
732
Z78486.1
Seq('CGTCACGAGGTTTCCGTAGGTGAATCTGCGGGAGGATCATTGTTGAGATCACAT...TGA')
731
Z78485.1
Seq('CTGAACCTGGTGTCCGAAGGTGAATCTGCGGATGGATCATTGTTGAGATATCAT...GTA')
735
Z78484.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGGGGAAGGATCATTGTTGAGATCACAT...TTT')
720
Z78483.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...GCA')
740
Z78482.1
Seq('TCTACTGCAGTGACCGAGATTTGCCATCGAGCCTCCTGGGAGCTTTCTTGCTGG...GCA')
629
Z78481.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...TGA')
572
Z78480.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...TGA')
587
Z78479.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...AGT')
700
Z78478.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTCCGGAAGGATCAGTGTTGAGATCACAT...GGC')
636
Z78477.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...TGC')
716
Z78476.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...CCC')
592
Z78475.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...GGT')
716
Z78474.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACGT...CTT')
733
Z78473.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...AGG')
626
Z78472.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...AGC')
737
Z78471.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...AGC')
740
Z78470.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...GTT')
574
Z78469.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...GTT')
594
Z78468.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCGCAT...GTT')
610
Z78467.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...TGA')
730
Z78466.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...CCC')
641
Z78465.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...TGC')
702
Z78464.1
Seq('CGTAACAAGGTTTCCGTAGGTGAGCGGAAGGGTCATTGTTGAGATCACATAATA...AGC')
733
Z78463.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGTTCATTGTTGAGATCACAT...AGC')
738
Z78462.1
Seq('CGTCACGAGGTCTCCGGATGTGACCCTGCGGAAGGATCATTGTTGAGATCACAT...CAT')
736
Z78461.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTCCGGAAGGATCATTGTTGAGATCACAT...TAA')
732
Z78460.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTCCGGAAGGATCATTGTTGAGATCACAT...TTA')
745
Z78459.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...TTT')
744
Z78458.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...TTG')
738
Z78457.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTCCGGAAGGATCATTGTTGAGATCACAT...GAG')
739
Z78456.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...AGC')
740
Z78455.1
Seq('CGTAACCAGGTTTCCGTAGGTGGACCTTCGGGAGGATCATTTTTGAGATCACAT...GCA')
745
Z78454.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...AAC')
695
Z78453.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...GCA')
745
Z78452.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...GCA')
743
Z78451.1
Seq('CGTAACAAGGTTTCCGTAGGTGTACCTCCGGAAGGATCATTGTTGAGATCACAT...AGC')
730
Z78450.1
Seq('GGAAGGATCATTGCTGATATCACATAATAATTGATCGAGTTAAGCTGGAGGATC...GAG')
706
Z78449.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...TGC')
744
Z78448.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...AGG')
742
Z78447.1
Seq('CGTAACAAGGATTCCGTAGGTGAACCTGCGGGAGGATCATTGTTGAGATCACAT...AGC')
694
Z78446.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTCCGGAAGGATCATTGTTGAGATCACAT...CCC')
712
Z78445.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...TGT')
715
Z78444.1
Seq('CGTAACAAGGTTTCCGTAGGGTGAACTGCGGAAGGATCATTGTTGAGATCACAT...ATT')
688
Z78443.1
Seq('CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACAT...AGG')
784
Z78442.1
Seq('GTAGGTGAACCTGCGGAAGGATCATTGTTGAGATCACATAATAATTGATCGAGT...AGT')
721
Z78441.1
Seq('GGAAGGTCATTGCCGATATCACATAATAATTGATCGAGTTAATCTGGAGGATCT...GAG')
703
Z78440.1
Seq('CGTAACAAGGTTTCCGTAGGTGGACCTCCGGGAGGATCATTGTTGAGATCACAT...GCA')
744
Z78439.1
Seq('CATTGTTGAGATCACATAATAATTGATCGAGTTAATCTGGAGGATCTGTTTACT...GCC')
592

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