03.21

2022.02.14/biopython7.py

+#!/usr/bin/env python
+
+from Bio import SeqIO
+# ExPASy for obtaining records from ExPASy/Swiss-Prot
+from Bio import ExPASy
+from Bio import pairwise2
+from Bio.pairwise2 import format_alignment
+
+# get sequence 1
+socketObj1 = ExPASy.get_sprot_raw( "P00740" )
+proteinObj1 = SeqIO.read( socketObj1, "swiss" )
+socketObj1.close()
+
+# get sequence 2
+socketObj2 = ExPASy.get_sprot_raw( "P00748" )
+proteinObj2 = SeqIO.read( socketObj2, "swiss" )
+socketObj2.close()
+
+# show the information we've obtained
+#print( proteinObj1.description )
+#print( proteinObj1.seq )
+#print( proteinObj2.description )
+#print( proteinObj2.seq )
+
+# finding alignments
+alignments = pairwise2.align.globalxx(proteinObj1.seq, proteinObj2.seq)
+  
+# showing results
+for alignment in alignments:
+    print(format_alignment(*alignment))
\ No newline at end of file

2022.03.09/MSA.sequences.fasta

+>441E-1189 wei8feb28/441E1189.SEQ trimmed vector-stripped
+GCACTCCACCAGTAAAGAAGTGCAGGCAACTAGCTAGCTAACCATGGCCGCCTCTGCCTC
+TTGCATTTCACTGGTGGTGCTCGTGGCTCTGGCCACGGTGGCGTCGGCGCAGCTGTCGCC
+GACGTTCTACGACACGTCGTGCCCCAGGGCCCTGGCCACCATCAAGAGCGGCGTCATGGC
+CGCCGTGAGCAGCGACCCTCGGATGGGCGCGTCGCTGCTCCGGCTGCACTTCCACGACTG
+CTTCGTCCAAGGCTGTGACGCGTCTGTTCTGCTGTCTGGCATGGAACAAAACGCTCTCCC
+GAACAACGGGTCACTGCGGGGCTTCGGCGTCATCGACAGCATCAAGACACAGATCGAGGC
+CATCTGCGCCCAGACCGTCTCCTGCGCCGACATCCTCACCGTCGCTGCCCGTGACTCCGT
+CGTCGCCCTCGGAGGGCCATCATGGACAGTCCCTCTGGGAAGAAGGGATTCCATAGATGC
+AAACGAGGCGGCGGCAAACANCGACCTCCCANGCCCTACGTCTANCCGTTCAGATCTTGA
+NCTGGCATTCAGCAACAAGGGCCTCCTTACGGNCGACATGGTGGNCCTCTCCGGCGGCGC
+ANACCATCNGNCAAGGCGCANTGNCGGGNANCTTNAAAGGACAAGGATCTTACAAATGGA
+GACCCAANATTCGACCNACNAACCTTCNGCCCAANTTCTTNTTCCGGGGCCAAAATTGGC
+CCCCCGG
+>441E-1197 wei8feb28/441E1197.SEQ trimmed vector-stripped
+GCACCACTCCACCAGTAAAGAAGTGCAGGCAACTAGCTAGCTAACCATGGCCGCCTCTGC
+CTCTTGCATTTCACTGGTGGTGCTCGTGGCTCTGGCCACGGTGGCGTCGGCGCAGCTGTC
+GCCGACGTTCTACGACACGTCGTGCCCCAGGGCCCTGGCCACCATCAAGAGCGGCGTCAT
+GGCCGCCGTGAGCAGCGACCCTCGGATGGGCGCGTCGCTGCTCCGGCTGCACTTCCACGA
+CTGCTTCGTCCAAGGCTGTGACGCGTCTGTTCTGCTGTCTGGCATGGAACAAAACGCTCT
+CCCGAACAACGGGTCACTGCGGGGCTTCGGCGTCATCGACAGCATCAAGACACAGATCGA
+GGCCATCTGCGCCCAGACCGTCTCCTGCGCCGACATCCTCACCGTCGCTGCCCGTGACTC
+CGTCGTCGCCCTCGGAGGGCCATCATGGACAGTCCCTCTGGGAAGAAGGGATTCCATANA
+TGNAAACGAGGNGGTGGCAAACAGCGACTCCCAGCCCTACGTCTAGCCGTTCAGATCTTG
+AG
+>441E-186 Oct_13-2001/RH101257.SEQ trimmed vector-stripped [poly-A tail removed]
+GAGGCAACTAGCTAGCTAACCATGGCCGCCTCTGCCTCTTGCATTTCACTGGTGGTGCTC
+GTGGCTCTGGCCACGGTGGCGTCGGCGCAGCTGTCGCCGACGTTCTACGACACGTCGTGC
+CCCAGGGCCCTGGCCACCATCAAGAGCGGCGTCATGGCCGCCGTGAGCAGCGACCCTCGG
+ATGGGCGCGTCGCTGCTCCGGCTGCACTTCCACGACTGCTTCGTCCAAGGCTGTGACGCG
+TCTGTTCTGCTGTCTGGCATGGAACAAAACGCTCTCCCGAACAACGGGTCACTGCGGGGC
+TTCGGCGTCATCGACAGCATCAAGACACAGATCGAGGCCATCTGCGCCCAGACCGTCTCC
+TGCGCCGACATCCTCACCGTCGCTGCCCGTGACTCCGTCGTCGCCCTCGGAGGGCCATCA
+TGGACAGTCCCTCTGGGAAGAAGGGATTCCATAGATGCAAACGAGGCGGCGGCAAACAGC
+GACCTCCCAGGCCCTACGTCTAGCCGTTCAGATCTTGAGCTGGCATTCAGCAACAAGGGC
+CTCCTTACGGTCGACATGGTGGCCCTCTCCGGCGCGCACACCATCGGCCAGGCGCAGTGC
+GGGACCTTCAAGGACAGGATCTACAAATGGAGACCAAACATCGACACGACCTTCGCCCAC
+ATTCTTCTTCCGGGGCCAAACTGGCCCCCCGGGTNCCGGGCGGGCGGAACGGGCAACCCT
+GGGGGGAAACCTGGGAACACGAACGNACNGGGCCCAAACAACCNTTTCCGAACCAAAACG
+GCCCCTTAACTTAACAACCCNAAACCCTTCCCATTGGGTTCANCAAANAAAANGGGGGGC
+NTTCCCTNGGCCACCTCCGGGGAAACCCAGGGGGGGGCTTGGNTTNCAAAACCAAAACGG
+AAACCANCCCCCCCCCGGAAACAAAANNACCGGGGTNNCCCGGGGNAAAACTTTTTTGGG
+GGGTNCCAAAAAACCCCCGGGGCCCGNGNAATTTTTTAANNNAAAGGGGGGGCCCNTTTT
+TNNCCGNAAAGNGGGGGCCCCATTTTGGATTTCC
+>441E-1086 Oct_25-2001/RH102623.Seq trimmed vector-stripped
+GAAGAAGTGCAGGCAACTAGCTAGCTAACCATGGCCGCCTCTGCCTCTTGCATTTCACTG
+GTGGTGCTCGTGGCTCTGGCCACGGTGGCGTCGGCGCAGCTGTCGCCGACGTTCTACGAC
+ACGTCGTGCCCCAGGGCCCTGGCCACCATCAAGAGCGGCGTCATGGCCGCCGTGAGCAGC
+GACCCTCGGATGGGCGCGTCGCTGCTCCGGCTGCACTTCCACGACTGCTTCGTCCAAGGC
+TGTGACGCGTCTGTTCTGCTGTCTGGCATGGAACAAAACGCTCTCCCGAACAACGGGTCA
+CTGCGGGGCTTCGGCGTCATCGACAGCATCAAGACACAGATCGAGGCCATCTGCGCCCAG
+ACCGTCTCCTGCGCCGACATCCTCACCGTCGCTGCCCGTGACTCCGTCGTCGCCCTCGGA
+GGGCCATCATGGACAGTCCCTCTGGGAAGAAGGGATTCCATAGATGCAAACGAGGCGGCG
+GCAAACAGCGACCTCCCAGGCCCTACGTCTAGCCGTTCAGATCTTGAGCTGGCATTCAGC
+AACAAGGGCCTCCTTACGGTCGACATGGTGGCCCTCTCCGGCGCGCACACCATCGGCCAG
+GCGCAGTGCGGGACTTCAAGGACAGGATCTACAATGAGACCAACATCGACACGACCTTCG
+CCACATCTCTCCGGGCCAACTTGCCCCGGTCCGGNGGCGAACGGCAGCCTGGCGAACCTG
+GACACGACGACGGCCAACACCTTCGACAACGCCTACTACACCAAC
+>441E-25 Sept_11-2001/YW091042.SEQ trimmed vector-stripped
+GCACCACTCCACCAGTAAAGAAGTGCAGGCAACTAGCTAGCTAACCATGGCCGCCTCTGC
+CTCTTGCATTTCACTGGTGGTGCTCGTGGCTCTGGCCACGGTGGCGTCGGCGCAGCTGTC
+GCCGACGTTCTACGACACGTCGTGCCCCAGGGCCCTGGCCACCATCAAGAGCGGCGTCAT
+GGCCGCCGTGAGCAGCGACCCTCGGATGGGCGCGTCGCTGCTCCGGCTGCACTTCCACGA
+CTGCTTCGTCCAAGGCTGTGACGCGTCTGTTCTGCTGTCTGGCATGGAACAAAACGCTCT
+CCCGAACAACGGGTCACTGCGGGGCTTCGGCGTCATCGACAGCATCAAGACACAGATCGA
+GGCCATCTGCGCCCAGACCGTCTCCTGCGCCGACATCCTCACCGTCGCTGCCCGTGACTC
+CGTCGTCGCCCTCGGAGGGCCATCATG
+>441E-536 Oct_25-2001/RH102519.Seq trimmed vector-stripped
+GCACCACCGCTCCAGTAAGAAGTGCAGGTAGCTAGTAAGCAGGCGTGGCTTTGCTCTTCA
+GCTCTTGTAGCTAGCTAGCTAACCATGGCCGCCTCTGCGTCCTGCATTTCTCTGGTGGTG
+CTCGTGGCTCTGGCCACGGCGGCGTCGGGGCAGCTGTCGCCGACGTTCTACGACACGTCG
+TGCCCCAGGGCTTTGGCCACCATCAAGAGCGGCGTCATGGCTGCCGTGAGCAGCGACCCT
+CGGATGGGTGCGTCACTGCTCCGGCTGCACTTCCACGACTGCTTCGTCCAAGGCTGCGAC
+GCGTCTGTTCTGCTGTCTGGCATGGAACAAAACGCTATCCCGAACGCAGGGTCGCTGAGG
+GGCTTCGGCGTCATCGACAGCATCAAGACGCAGATCGAGGCCATCTGTAATCAGACCGTC
+TCTTGCGCTGACATCCTCACCGTCGCCGCCCGCGACTCCGTCGTCGCCCTCGGGGGGCCC
+GTCATGGACAGTCCCTTTTGGGGAGAAGAGATTCCATAGATGCAAACGAGGCAGAGGCAA
+ACAGCGACCTTCCAGGCTTTAATTCTAGCCGCTCAGAGCTCGAGGCAGCATTCCTCAGGA
+AGGCGGACTCAATACGGTCGANATGGTGGGCCCTCTCGGCGG
+>441E-2504 08jan02wei5/441E2504.SEQ trimmed vector-stripped
+GTCCACCAGTAAAGAAGTGCAGGCAACTAGCTAGCTAACCATGGCCGCCTCTGCCTCTTG
+CATTTCACTGGTGGTGCTCGTGGCTCTGGCCACGGTGGCGTCGGCGCAGCTGTCGCCGAC
+GTTCTACGACACGTCGTGCCCCAGGGCCCTGGCCACCATCAAGAGCGGCGTCATGGCCGC
+CGNGAGCAGCGACCCTCGGATGGGCGCGTCGCTGCTCCGGNTGCACTTCCACGACTGCTT
+CGTCCAAGGCTGTGANNCGTCTGTTCTGNTGTCTGGCATGGAACAAAACGCTCTCCCGAA
+CAACGGGTCACTGCGGGGNTTCNGCGTCCATCGACAGCATNCAANACACAGATCGAGGCC
+ATCTGCGNCCAGACCGTCTCCTGCGCCGACATCCTCACCGNCNNTGCCCGNGACTCCGTC
+CNTCNTCCCTCGNAAGGATCTATACATGNACAGTCCCCTCTGGGNAAAAAACGCANNTTT
+NCNCAANNATCCCAACCNATAGNCGCAAGANNANACAACNACACGACCNNCACCTNANNA
+NCCCATNNNCANNCTAAGNCCGCTANACANCANNNANCTCANNCTCTNNCCAACTTACNT
+CTANNANNNATAAGCTACCCTTCATNTNTAACTNAGACACTGAACNNNNGGAGNTAGNGA
+CCAACNTCTCTCTCAGCACNNTACACANNNATNACTATCCANTATCGCCTCNATCTNCCA
+TCNTCACCTACAATNGAAGCCNCTNAANCACNCCCTNCTTCTTAANAGNGNTACTCTACT
+GCGCTNTCTCTACNTNANNCTCACAGCNTGCACACCTNCCTTNCCCACCTCACTNNGAGT
+ANAATNCNATACGTNAANNTCTNTCCTNTCTCCGCGACTCNACCAAAACANNNCNATNCT
+CTTTTCTTNTACNCAGCTTATNCTCCCATCTTANCTTTNTCNACCCTCAACCTCCCTCNA
+TCCANACNCCAACNNAANNGGNACNCTCANCTAANACNTAAAGTCCAANAAAACACACAT
+CTNNTNACNCTACCCATTCCCCCCCCCTCCCCACNCCCCCNNANTTCNCTCACNCNTTAC
+ACCACNCNNTTNCNCCNACTCAANTCCANCNCNTCATCCTCTATCCTANACTCANAAGCC
+TGCCACACCTTNTAACCCNTCCCTACTTTATNCACTAAACTCATNCNNCTACAATATGCN
+GNTNCACTCNCCNCCNATATACTNTACCTAAGCATTCTCCTCACACACA
+>441E-471 Nov_1601_20-2000/Nov1601/RH111624.Seq trimmed vector-stripped [poly-A tail removed]
+GCAGCGACCCTCGGATGGGCGCGTCGCTGCTCCGGCTGCACTTCCACGACTGCTTCGTCC
+AAGGCTGTGACGCGTCTGTTCTGCTGTCTGGCATGGAACAAAACGCTCTCCCGAACAACG
+GGTCACTGCGGGGCTTCGGCGTCATCGACAGCATCAAGACACAGATCGAGGCCATCTGCG
+CCCAGACCGTCTCCTGCGCCGACATCCTCACCGTCGCTGCCCGTGACTCCGTCGTCGCCC
+TCGGAGGGCCATCATGGACAGTCCCTCTGGGAAGAAGGGATTCCATAGATGCAAACGAGG
+CGGCGGCAAACAGCGACCTCCCAGGCCCTACGTCTAGCCGTTCAGATCTTGAGCTGGCAT
+TCAGCAACAAGGGCCTCCTTACGGTCGACATGGTGGCCCTCTCCGGCGCGCACACCATCG
+GCCAGGCGCAGTGCGGGACCTTCAAGGACAGGATCTACAATGAGACCAACATCGACACGA
+CCTTCGCCACATCTCTCCGGGCCAACTGCCCCCGGTCCGGCGGCGACGGCAGCCTGGCGA
+ACCTGGACACGACGACGGGCAACACCTTCGACAACGCCTACTACACCAACCTCATGTCAC
+AGAAAGGGCTNCTGCACTCCGANCAAGTGCTGTTCAACAACGACACCACCGACAACACGG
+TNCGGGAANTTTGCGTTCNAANCCGGNCGCANTTNAACAAGCGGCCNTTCACGAACGGGC
+CATTGGATCAANAATGGGGGAAANATTCGCGGCCCCAAAAAAAAGGGAACCCCANGGGGC
+CANAAATCANGGGNTCAACCTTTGGTTCCANGGGGNGGNAACTTCCCTGGANTTTTACGG
+GAACNAAACCCCCAACCCTACNTAATTCNGGGTTGGGGCCTTCCCC
+>441E-2320 wei7feb26/441E2320.SEQ trimmed vector-stripped
+GGCGCGTCGCTGCTCCGGCTGCACTTCCACGACTGCTTCGTCCAAGGCTGTGACGCGTCT
+GTTCTGCTGTCTGGCATGGAACAAAACGCTCTCCCGAACAACGGGTCACTGCGGGGCTTC
+GGCGTCATCGACAGCATCAAGACACAGATCGAGGCCATCTGCGCCCAGACCGTCTCCTGC
+GCCGACATCCTCACCGTCGCTGCCCGTGACTCCGTCGTCGCCCTCGGAGGGCCATCATGG
+ACAGTCCCTCTGGGAAGAAGGGATTCCATAGATGCAAACGAGGCGGCGGCAAACAGCGAC
+CTCCCAGGCCCTACGTCTAGCCGTTCAGATCTTGAGCTGGCATTCAGCAACAAGGGCCTC
+CTTACGGTCGACATGGTGGCCCTCTCCGGCGCGNACACCATCGGCCAGGCGCAGTGCGGG
+ACCTTCAAGGACAGGATCTACAATGAGACCAACATCGACACGACCTTCGCCACATCTCTC
+CGGGCCAACTGCCCCCGGTCCGGCGGCGACGGCAGCCTGGCGAACTGGACACGACGACGG
+CCAACACCTTCGACAACGCCTACTACACCAACCTCATGTCACAGAAGGGGGCTCCTGCAC
+TCGGACCAGGTGCTGNTCCACAACGACACCACCGACAACACGGTCCGGAACTTTGNCGTC
+CAACCCCGGCGCATTCNACAANCGCCTTTTCACGAACGGCCCAT
+>441E-877 Dec21wei3/Dec21wei3/441E877.SEQ trimmed vector-stripped
+GCTCCACCAGTAAAGAAGTGCAGGCAACTAGCTAGCTAACCATGGCCGCCTCTGCCTCTT
+GCATTTCACTGGTGGTGCTCGTGGCTCTGGCCACGGTGGCGTCGGCGCAGCTGTCGCCGA
+CGTTCTACGACACGTCGTGCCCCAGGGCCCTGGCCACCATCAAGAGCGGCGTCATGGCCG
+CCGTGAGCAGCGACCCTCGGATGGGCGCGTCGCTGCTCCGGCTGCACTTCCACGACTGCT
+TCGTCCAAGGCTGTGACGCGTCTGTTCTGCTGTCTGGCATGGAACAAAACGCTCTCCCGA
+ACAACGGGTCACTGCGGGGCTTCGGCGTCATCGACAGCATCAAGACACAGATCGAGGCCA
+TCTGCGCCCAGACCGTCTCCTGCGCCGACATCCTCACCGTCGCTGCCCGTGACTCCGTCG
+TCGCCCTCGGAGGGCCATCATGGACAGTCCCTCTGGGAAGAAGGGATTCCATAGATGCAA
+ACGAGGCGGCGGCAAACAGCGACCTCCCAGGCCCTACGTCTAGCCGTTCAGATCTTGAGC
+TGGCATTCAGCAACAAGGGCCTCCTTACGGTCGACATGGTGGCCTCTCCGGNGCGCACAC
+CATCGGNCAGGCGCAGTGCGGGACCTTCAAGGACAGGATCTACAATGAGACCAACATCGA
+CACGACCTTCGCCACATCTCTTCCGGGCCAAACTGCCCCCGGTCCCGGCGGNNGACGGNC
+AANCCCNGNGCGNAACCTTGGGAAACCNAANGACGGCCCCAACAACCCTTC
+>441E-532 Oct_17-2001/RH101614.SEQ trimmed vector-stripped
+GCCACCACTCCACCAGTAAAGAAGTGCAGGCAACTANNTAGCTAACCATGGCCGCCTCTG
+CCTCTTGCATTTCACTGGTGGTGCTCGNGGCTCTGGCCACGGTGGCGTCGGCGCAGCTGT
+CGCCGACGTTCTACGACACGTCGTGCCCCAGGGCCCTGGCCACCATCAAGAGCGGCGTCA
+TGGCCGCCGTGAGCAGCGACCCTCGGATGGGCGCGTCGCTGCTCCGGCTGCACTTCCACG
+ACTGCTTCGTCCAAGGCTGTGACGCGTCTGTTCTGCTGTCTGGCATGGAACAAAACGCTC
+TCCCGAACAACGGGTCACTGCGGGGCTTCGGCGTCATCGACAGCATCAAGACACAGATCG
+AGGCCATCTGCGCCCAGACCGTCTCCTGCGCCGACATCCTCACCGTCGCTGCCCGTGACT
+CCGTCGTCGCCCTCGGAGGGCCATCATGGACAGTCCCTCTGGGAAGAAGGGATTCCATAG
+ATGCAAACGAGGCGGCGGCAAACAGCGACCTCCCAGGCCCTACGTCTAGCCGTTCAGATC
+TTGAGCTGGCATTCAGCAACAAGGGCCTCCTTACGGTCGACATGGTGGGCCCTCTCCGGC
+GCGCACACCATCGGNCAGGCGCAGTGCGGGGACCTTCAAGGACAGGATTTTACAATGANA
+CCAACATCGAACACGACCTTCGCCACATTCTCTTCCGGGGCCAANTGCCCCCGGTCCGGN
+GGGNGACGGGCAGCCTGGCGAAACCTGGGACACGAAAGACNGNCCAACACCTTCGANAAA
+GGCNTACTTACAACAAACCTTCATGGTNNCAGAAAAGGGCTTCCTGGCACTCGGAC
+>441E-1102 Oct_25-2001/RH102501.Seq trimmed vector-stripped
+GCCGCTCCAGTAAGAAGTGCAGGTAGCTAGTAAGCAGGCGTGGCTTTGCTCTTCAGCTCT
+TGTAGCTAGCTAGCTAACCATGGCCGCCTCTGCGTCCTGCATTTCTCTGGTGGTGCTCGT
+GGCTCTGGCCACGGCGGCGTCGGGGCAGCTGTCGCCGACGTTCTACGACACGTCGTGCCC
+CAGGGCTTTGGCCACCATCAAGAGCGGCGTCATGGCTGCCGTGAGCAGCGACCCTCGGAT
+GGGTGCGTCACTGCTCCGGCTGCACTTCCACGACTGCTTCGTCCAAGGCTGCGACGCGTC
+TGTTCTGCTGTCTGGCATGGAACAAAACGCTATCCCGAACGCAGGGTCGCTGAGGGGCTT
+CGGCGTCATCGACAGCATCAAGACGCAGATCGAGGCCATCTGTAATCAGACCGTCTCTTG
+CGCTGACATCCTCACCGTCGCCGCCCGCGACTCCGTCGTCGCCCTCGGGGGGCCGTCATG
+GACAGTCCCTTTGGGGAGAAGAGATTCCATAGATGCAAACGAGGCAGAGGCAAACAGCGA
+CCTTCCAGGCTTTAATTCTAACCGCTCANAGCTCGAGGCAGCATTCCTCAGGAAAGGCGG
+ACTCAATACGGTCGACATGGTGGGCCTCTCGGGCGCGCACACATCGGCCAGGCGCAATGC
+TCGACTTCCGGGCTCGGATCTACGGCGGTGGACACCAACATCAATG

2022.03.21/NC_001675.fasta

+>Cyanophora NC_001675 Cyanophora paradoxa cyanelle
+ATGGCAAGACAGAAATTTGACGGAAATAAACCACATGTAAACATTGGTACTATTGGTCACGTTGACCATG
+GAAAAACTACCTTAACTGCTGCAATTACAACTGCTCTAGCATCCCAAGGTAAAGGAAAAGCTCGTAAATA
+TGATGAAATTGATGCTGCTCCAGAAGAAAAAGCACGTGGTATTACTATTAATACTGCACACGTAGAATAT
+GAGACTGAAAAACGTCATTATGCACACGTAGATTGCCCAGGACACGCAGATTATGTGAAAAACATGATTA
+CAGGTGCAGCTCAAATGGACGGAGCTATTTTAGTTGTTTCTGCAGCTGATGGTCCAATGCCTCAAACTCG
+TGAACATATTCTGTTAGCAAAACAAGTTGGTGTTCCGAACATGGTTGTTTTCTTAAATAAAGAAGACCAA
+ATTGATGACGCTGATTTATTAGAATTAGTAGAATTAGAAGTTCGTGAATTATTAAGCAAATATGATTTCC
+CAGGTGATCAAATTCCGTTCGTTAGTGGTTCTGCGTTATTAGCTTTAGAAAGTCTAAGTTCTAATCCAAA
+ACTTATGCGTGGCGAAGATAAATGGGTAGATAAAATTCTTGCTTTAATGGATGCAGTTGATGAATATATT
+CCTACTCCAGAACGTCCAATCGATAAATCTTTCTTAATGGCAATTGAAGATGTTTTCTCTATTACCGGTC
+GTGGTACAGTAGCTACTGGTAGAATTGAAAGAGGTGCTATTAAGGTTGGTGAAACAGTTGAATTAGTAGG
+TTTAAAAGATACTAAATCAACAACAGTTACTGGTTTAGAAATGTTCCAAAAAACATTAGAAGAAGGGATG
+GCTGGTGATAACATCGGTATTCTTCTTCGTGGTGTTCAAAAAACTGATATTGAGCGTGGTATGGTTTTAG
+CAAAACCAGGTTCTATTACTCCACATACTCAATTTGAATCTGAAGTTTATGTATTAACAAAAGATGAAGG
+TGGTCGTCATACTCCATTCTTCTCTGGATATCGTCCACAATTTTATGTACGTACTACTGATGTTACTGGT
+AGCATTGATGCGTTTACTGCAGATGATGGTAGTAATGCAGAAATGGTTATGCCAGGAGATCGTATTAAAA
+TGACAGTAAGTTTAGTACATCCAATTGCGATTGAACAAGGTATGCGTTTCGCGATTCGTGAAGGTGGTCG
+TACAATTGGTGCAGGTGTAGTTTCTAAGATTTTAAAATAA

2022.03.21/NC_004116.fasta

+>Streptococcus NC_004116:757604..758800 Streptococcus agalactiae 2603V/R 
+ATGGCAAAAGAAAAATACGATCGTAGTAAACCACACGTTAACATTGGTACAATCGGACACGTTGACCACG
+GTAAAACTACTTTAACAGCAGCTATCACAACTGTATTGGCACGTCGCTTGCCTACTTCAGTTAACCAACC
+AAAAGATTACGCTTCTATCGATGCTGCTCCAGAAGAGCGCGAACGCGGAATCACAATCAACACTGCACAC
+GTTGAGTACGAAACTGAAAAACGTCACTATGCCCACATCGACGCTCCAGGACACGCGGACTACGTTAAAA
+ACATGATCACTGGTGCTGCTCAAATGGACGGAGCTATCCTTGTAGTTGCTTCAACTGATGGACCAATGCC
+ACAAACTCGTGAGCACATCCTTCTTTCACGTCAAGTTGGTGTTAAACACCTTATCGTATTCATGAACAAA
+GTTGACCTTGTTGATGATGAAGAATTGCTTGAATTGGTTGAAATGGAAATTCGTGACCTTCTTTCAGAAT
+ACGACTTCCCAGGTGATGACCTTCCAGTTATCCAAGGTTCAGCTCTTAAAGCACTTGAAGGCGACGAAAA
+ATACGAAGACATCATCATGGAATTGATGAGCACTGTTGATGAGTACATTCCAGAACCAGAACGTGATACT
+GACAAACCTTTACTTCTTCCAGTTGAAGATGTATTCTCAATCACTGGACGTGGTACAGTTGCTTCAGGAC
+GTATCGACCGTGGTACTGTTCGTGTCAACGACGAAGTTGAAATCGTTGGTATTAAAGAAGATATCCAAAA
+AGCAGTTGTTACTGGTGTTGAAATGTTCCGTAAACAACTTGACGAAGGTCTTGCAGGGGACAACGTTGGT
+GTTCTTCTTCGTGGTGTTCAACGTGATGAAATCGAACGTGGTCAAGTTCTTGCTAAACCAGGTTCAATCA
+ACCCACACACTAGATTTAAAGGTGAAGTTTACATCCTTTCTAAAGAAGAAGGTGGACGTCATACTCCATT
+CTTCAACAACTACCGTCCACAATTCTACTTCCGTACAACTGACGTAACAGGTTCAATCGAACTTCCAGCA
+GGAACAGAAATGGTTATGCCTGGTGATAACGTTACTATCGAAGTTGAATTGATTCACCCAATCGCCGTAG
+AACAAGGTACTACTTTCTCAATCCGTGAAGGTGGACGTACTGTTGGTTCAGGTATCGTTTCAGAAATCGA
+AGCTTAA
+

2022.03.21/NC_004741.fasta

+>Shigella NC_004741 Shigella flexneri 2a str. 2457T
+ATGTCTAAAGAAAAGTTTGAACGTACAAAACCGCACGTTAACGTCGGTACTATCGGCCACGTTGACCATG
+GTAAAACAACGCTGACCGCTGCAATCACTACCGTACTGGCTAAAACCTACGGCGGTGCTGCTCGCGCATT
+CGACCAGATCGATAACGCGCCGGAAGAAAAAGCTCGTGGTATCACCATCAACACTTCTCACGTTGAATAC
+GACACCCCGACCCGTCACTACGCACACGTAGACTGCCCGGGGCACGCCGACTATGTTAAAAACATGATCA
+CCGGTGCTGCTCAGATGGACGGCGCGATCCTGGTAGTTGCTGCGACTGACGGCCCGATGCCGCAGACTCG
+TGAGCACATCCTGCTGGGTCGTCAGGTAGGCGTTCCGTACATCATCGTGTTCCTGAACAAATGCGACATG
+GTTGATGACGAAGAGCTGCTGGAACTGGTTGAAATGGAAGTTCGTGAACTTCTGTCTCAGTACGACTTCC
+CGGGCGACGACACTCCGATCGTTCGTGGTTCTGCTCTGAAAGCGCTGGAAGGCGACGCAGAGTGGGAAGC
+GAAAATCCTGGAACTGGCTGGCTTCCTGGATTCTTACATTCCGGAACCAGAGCGTGCGATTGACAAGCCG
+TTCCTGCTGCCGATCGAAGACGTATTCTCCATCTCCGGTCGTGGTACCGTTGTTACCGGTCGTGTAGAAC
+GCGGTATCATCAAAGTTGGTGAAGAAGTTGAAATCGTTGGTATCAAAGAGACTCAGAAGTCTACCTGTAC
+TGGCGTTGAAATGTTCCGCAAACTGCTGGACGAAGGGCGTGCTGGTGAGAACGTAGGTGTTCTGCTGCGT
+GGTATCAAACGTGAAGAAATCGAACGTGGTCAGGTACTGGCTAAGCCGGGCACCATCAAGCCGCACACCA
+AGTTCGAATCTGAAGTGTACATTCTGTCCAAAGATGAAGGCGGTCGTCATACTCCGTTCTTCAAAGGCTA
+CCGTCCGCAGTTCTACTTCCGTACTACTGACGTGACTGGTACCATCGAACTGCCGGAAGGCGTAGAGATG
+GTAATGCCGGGCGACAACATCAAAATGGTTGTTACCCTGATCCACCCGATCGCGATGGACGACGGTCTGC
+GTTTCGCAATCCGTGAAGGCGGCCGTACCGTTGGCGCGGGCGTTGTAGCAAAAGTTCTGAGCTAA

2022.03.21/NC_008027.fasta

+>Pseudomonas NC_008027.1 Pseudomonas entomophila L48 
+GTGGCTAAAGAAAAATTTGATCGTTCCCTTCCCCACGTTAACGTCGGCACTATCGGCCACGTTGACCACG
+GTAAGACCACTCTGACCGCAGCTCTGACTCGCGTCTGCTCCGAAGTTTTCGGTTCGGCCGTCGTTGAGTT
+CGACAAGATCGACTCGGCTCCAGAAGAAAAAGCGCGCGGTATCACCATCAACACCGCTCACGTCGAGTAC
+AACTCGAACATTCGTCACTACGCTCACGTTGACTGCCCAGGTCACGCTGACTACGTGAAGAACATGATCA
+CCGGTGCTGCCCAGATGGACGGCGCGATCCTGGTTTGCTCGGCCGCCGATGGTCCGATGCCACAAACCCG
+TGAGCACATCCTGCTGTCCCGTCAGGTTGGCGTTCCGTACATCGTGGTCTTCCTGAACAAGGCTGACCTG
+GTAGATGACGCTGAGCTGCTGGAACTGGTCGAGATGGAAGTTCGCGACCTGCTGTCCACCTACGACTTCC
+CAGGCGACGACACCCCGATCATCATCGGTTCGGCTCGTATGGCGCTGGAAGGCAAAGACGACAACGAAAT
+GGGCACTACCGCTGTCAAGAAGCTGGTAGAAACTCTGGATGCCTACATCCCTGAGCCAGTTCGTGCCATC
+GACCAGCCGTTCCTGATGCCGATCGAAGACGTATTCTCGATCTCGGGTCGTGGTACCGTTGTTACCGGCC
+GTATCGAGCGTGGTATCGTCCGCGTTCAAGACCCGCTGGAAATCGTTGGTCTGCGTGACACCACCACCAC
+CACCTGCACCGGCGTTGAGATGTTCCGCAAGCTGCTGGACGAAGGTCGTGCTGGCGAGAACTGCGGCGTC
+CTGCTGCGTGGTACCAAGCGTGACGACGTTGAGCGTGGCCAGGTTCTGGTCAAGCCAGGTTCGGTCAAGC
+CGCACACCAAGTTCACCGCAGAAGTCTACGTCCTGTCGAAGGAAGAAGGCGGTCGTCACACTCCGTTCTT
+CAAAGGCTACCGTCCTCAGTTCTACTTCCGTACCACTGACGTGACCGGTAACTGCGAGCTGCCGGAAGGC
+GTTGAAATGGTAATGCCAGGTGACAACATTCAGATGACTGTCACCCTGATCAAGACCATCGCAATGGAAG
+ACGGTCTGCGCTTCGCCATCCGTGAAGGCGGTCGTACCGTCGGCGCCGGCGTCGTAGCCAAAATCATCGA
+GTAA

2022.03.21/NC_008095.fasta

+>Myxococcus NC_008095.1 Myxococcus xanthus DK 1622 
+ATGGCCAAGGAGAAGTTCGAGCGTAACAAGCCCCACGTGAACATCGGCACGATCGGACACGTGGACCACG
+GCAAGACGTCGCTGACGGCCGCCATCACCAAGGTGCTGGCGAAGACGGGCGGCGCCACGTTCCTGGCGTA
+CGACCTGATTGACAAGGCGCCGGAGGAGCGTGAGCGCGGTATCACGATTTCCACCTCGCACGTGGAGTAC
+CAGACGTCGAACCGGCACTACGCCCACGTCGACTGTCCGGGCCACGCCGACTACGTGAAGAACATGATCA
+CGGGCGCGGCGCAGATGGACGGCGCCATCCTGGTGGTGTCGGCGGCGGACGGCCCGATGCCGCAGACGCG
+TGAGCACATCCTGCTGGCGCGCCAGGTCGGCGTTCCGTACATCGTGGTCTTCCTGAACAAGGTGGACATG
+CTGGACGACCCCGAGCTGCGCGAGCTCGTGGAGATGGAAGTCCGCGACCTGCTGAAGAAGTACGAGTTCC
+CTGGCGATGACATCCCCATCATCCCGGGCTCGGCGCTGAAGGCGCTGGAGGGTGACACCAGCGACATCGG
+CGAGCCGGCCATCCTGAAGCTGATGGAGGCGGTGGACAGCTACATCCCGACGCCGCAGCGCGCGACGGAC
+AAGCCCTTCCTGATGCCGGTGGAGGACGTGTTCTCCATCTCCGGCCGCGGCACGGTGGCCACGGGCCGCG
+TCGAGCGCGGTATCATCAAGGTCGGCGAGGAAGTGGAAGTCGTTGGTCTGCGCCCGACGCAGAAGACGGT
+CGTCACGGGCGTGGAGATGTTCCGCAAGCTGCTGGACCAGGGCATGGCGGGCGACAACATCGGCGCGCTG
+GTGCGCGGCCTGAAGCGCGAGGACATGGAGCGCGGCCAGGTGCTGGCCAAGCCGGGCAGCATCACCCCGC
+ACACCAAGTTCAAGGCGCAGATCTACGTGCTGTCGAAGGAAGAGGGCGGTCGTCACACCCCGTTCTTCAA
+GGGCTACCGCCCGCAGTTCTACTTCCGCACCACGGACGTGACGGGCTCGGTGAAGCTGCCGGAGAACGTC
+GAAATGGTGATGCCGGGCGACAACATCGCCATCGAGGTGGAGCTCATCACCCCCGTGGCCATGGAGAAGG
+AGCTGCGCTTCGCTGTTCGCGAGGGTGGCCGCACCGTGGGCGCCGGCGTCGTGGCGGAAATCATCGAGTA
+A

2022.03.21/NC_010280.fasta

+>Chlamydia NC_010280 Chlamydia trachomatis L2b/UCH-1/proctitis
+ATGTCAAAAGAAACTTTTCAACGTAATAAGCCTCATATCAACATAGGGACCATTGGCCACGTTGACCATG
+GTAAGACTACGTTGACAGCTGCTATTACGCGTACGTTGTCTGGAGATGGGTTGGCTGATTTTCGTGATTA
+TAGCTCTATTGACAACACTCCTGAAGAAAAAGCTCGCGGTATTACAATTAACGCTTCCCACGTTGAGTAC
+GAAACAGCTAATCGTCACTACGCTCACGTGGACTGCCCTGGTCACGCTGACTATGTTAAAAACATGATCA
+CCGGTGCGGCTCAAATGGACGGGGCTATTCTAGTAGTTTCTGCAACAGACGGAGCTATGCCTCAAACTAA
+AGAGCATATTCTTTTGGCAAGACAAGTTGGGGTTCCTTACATCGTTGTTTTTCTCAATAAAATTGACATG
+ATTTCCGAAGAAGACGCTGAATTGGTCGACTTGGTTGAGATGGAGTTGGCTGAGCTTCTTGAAGAGAAAG
+GATACAAAGGGTGTCCAATCATCAGAGGTTCTGCTCTGAAAGCTTTGGAAGGGGATGCTGCATACATAGA
+GAAAGTTCGAGAGCTAATGCAAGCCGTCGATGATAATATCCCTACTCCAGAAAGAGAAATTGACAAGCCT
+TTCTTAATGCCCATTGAGGACGTGTTCTCTATCTCCGGACGAGGAACTGTAGTAACTGGACGTATTGAGC
+GTGGAATTGTTAAAGTTTCCGATAAAGTTCAGTTGGTCGGTCTTAGAGATACTAAAGAAACGATTGTTAC
+TGGGGTTGAAATGTTCAGAAAAGAACTCCCAGAAGGTCGTGCAGGAGAGAATGTTGGATTGCTCCTCAGA
+GGTATTGGTAAGAACGATGTGGAAAGAGGAATGGTTGTTTGCTTGCCAAACAGTGTTAAACCTCATACAC
+GGTTTAAGTGTGCTGTTTACGTTCTGCAAAAAGAAGAAGGTGGACGACATAAGCCTTTCTTCACAGGATA
+TAGACCTCAATTCTTCTTCCGTACAACAGACGTTACAGGTGTGGTAACTCTGCCTGAGGGAGTTGAGATG
+GTCATGCCTGGGGATAACGTTGAGTTTGAAGTGCAGTTGATTAGCCCTGTGGCTTTAGAAGAAGGTATGA
+GATTTGCGATTCGTGAAGGTGGTCGTACAATCGGTGCTGGAACTATTTCTAAGATCATTGCATAA

2022.03.21/NC_013893.fasta

+>Staphylococcus NC_013893 Staphylococcus lugdunensis HKU09-01
+ATGGCAAAAGAAAAATTCGATCGCTCAAAAGAACATGCCAATATTGGTACTATCGGTCACGTTGACCATG
+GTAAAACTACTTTAACAGCTGCAATTGCAACTGTATTAGCAAAAAATGGTGACACTGTAGCACAATCATA
+CGACATGATTGACAACGCTCCAGAAGAAAAAGAACGTGGTATTACAATCAATACTGCACACATCGAATAT
+CAAACTGATAAACGTCACTATGCGCACGTTGACTGCCCAGGACACGCTGACTATGTTAAAAACATGATCA
+CTGGTGCTGCTCAAATGGACGGCGGTATCTTAGTAGTTTCTGCTGCAGATGGTCCAATGCCACAAACTCG
+TGAACACATTCTTTTATCACGTAACGTTGGTGTGCCAGCATTAGTAGTATTCTTAAACAAAGTTGACATG
+GTTGACGATGAAGAATTATTAGAATTAGTAGAAATGGAAGTTCGTGATTTATTAACTGAATATGACTTCC
+CAGGTGACGATGTGCCTGTAATCGCTGGTTCAGCATTAAAAGCTTTAGAAGGCGACGAAAAATACGAAGC
+TAAAATCTTAGAATTAATGGATGCAGTTGATAACTACATTCCAACTCCAGAACGTGACTCTGACAAACCA
+TTCATGATGCCAGTTGAGGACGTATTCTCAATCACTGGTCGTGGTACTGTTGCTACAGGCCGTGTTGAAC
+GTGGTCAAATCAAAGTCGGTGAAGAAGTTGAAATTATTGGTATCCACGATACTACTAAAACAACGGTTAC
+TGGTGTAGAAATGTTCCGTAAATTATTAGACTATGCTGAAGCTGGTGACAACATCGGTGCGTTATTACGT
+GGTGTTGCTCGTGAAGATGTACAACGTGGACAAGTATTAGCTGCTCCAGGTTCAATTACACCTCACACTA
+AATTTAAAGCTGACGTATATGTTTTATCTAAAGATGAAGGTGGACGTCATACACCATTCTTCTCAAACTA
+CCGTCCACAATTCTATTTCCGTACTACAGACGTAACTGGTGTTGTTAACTTACCAGAAGGTACAGAAATG
+GTTATGCCTGGTGACAACGTTGAAATGACAGTTGAATTAATCGCTCCAATCGCTATCGAAGACGGAACTC
+GTTTCTCAATTCGTGAAGGTGGACGTACTGTAGGATCAGGCGTTGTAACTGAAATTATGGAATAA

2022.03.21/NC_014014.fasta

+>Mycoplasma NC_014014 Mycoplasma crocodyli MP145
+ATGGCAAAAATAGATTTTGACCGTAGCAAAGAACACGTTAACGTTGGAACAATCGGACACGTTGACCATG
+GAAAAACAACTTTAACAGCTGCAATTGCTACAGTTTTATCAAAAAAAGGATTATCAGAAGCTCGTGATTA
+TGCTTCAATCGATAATGCACCAGAAGAAAAAGCACGTGGGATAACAATTAATACTTCACACGTTGAATAT
+CAAACAGAAAAACGTCACTACGCACACGTTGACTGTCCTGGTCACGCTGACTACGTTAAAAACATGATTA
+CCGGAGCAGCTCAAATGGATGGAGCAATCTTAGTTGTTGCTGCAACAGATGGACCAATGCCTCAAACAAA
+AGAACACATTCTTTTATCAAGACAAGTTGGAGTTCCTCGTATTGTTGTTTTCTTAAACAAATGCGACATG
+CTACAAGGTAAAGACGGTGAAGAAATGATCGACCTTGTTGAAATGGAAATACGTGGATTATTATCAGAAT
+ACGGATTTGATGGAGATAATGCACCAGTTGTTCGTGGATCAGCATTACAAGCTTTACAAGGAAATGCAGA
+ATACGAAGACAAAATTATGGAATTAATGTCTGCGGTTGATGAATACATTTTAACACCTCAAAAAGACTTA
+GACAAACCATTCTTAATGGCCGTTGAAGACGTTTTCACAATTACAGGACGTGGAACTGTTGCTACAGGAC
+GTGTAGAACGTGGAACATTAAAATTAAATGATGAAGTTGAAATTGTTGGGTTACACGCAACTAAAAAAAC
+AGTTGTTACAGGAATTGAAATGTTCCGTAAAAACTTAAAAGAAGCTTTAGCTGGGGATAATGCAGGATTA
+TTACTACGTGGAATTAACCGTGAAGATGTAGAACGTGGACAAGTATTAGCTAAACCAGGTTCAATTATTC
+CTCACACAGAATTCGAAGCTGCAATTTATGTACTTAAAAAAGAAGAAGGTGGACGTCATACACCATTCTT
+AAAGAACTATAAACCTCAATTCTACTTCCGTACAACAGACGTTACTGGTGGAGTTGAATTCGAAGCTGGA
+CGTGAAATGGTTATGCCAGGAGAAAATGTTAACTTAAAAGTTAAACTTATTGCTCCTATCGCTGTTGAAG
+CAGGAACAAAATTCTCTATCCGTGAAGGTGGACGTACAGTTGGTGCTGGTTCAGTAACAAAAATTATTAA
+ATAA

biopython-examples/biopython4_log.txt

@@ -15,3 +15,4 @@ bash-4.4$
 
 bash-4.4$ ./biopython4.py
 bash-4.4$ 
+ 
\ No newline at end of file

biopython-examples/biopython5.py

@@ -12,7 +12,7 @@ Entrez.email = "binfo200@cs.usask.ca"
 # and the accession number to look for is DQ091202.  It happens to be
 # the record for the Elephas maximus HBB/D gene.
 socketObj = Entrez.efetch( db="nucleotide", rettype="fasta",
-                           id="DQ091202" )
+                           id="M62653" )
 # the above creates a socket object that works like a typical file object.
 # Hence we can use SeqIO to read from it.
 

python-examples/dec_Marrus_claudanielis.txt

+dive	depth	latitude	longitude	date	comment
+Tiburon 596	1190	  36.60200	-122.37467	19-Jul-03	holotype
+JSL II 1411	 518	  39.94000	 -70.23833	16-Sep-86	paratype
+JSL II 930	 686	  40.08383	 -69.05017	18-Aug-84	Youngbluth (1989)
+Ventana 1575	 767	  36.70400	-122.04200	11-Mar-99	
+Ventana 1777	 934	  36.71000	-122.04500	16-Jun-00	
+Ventana 2243	1001	  36.70800	-122.06400	 9-Sep-02	
+Tiburon 515	1156	  36.70000	-122.03300	24-Nov-02	
+Tiburon 531	1144	  24.31700	-109.20300	13-Mar-03	
+Tiburon 547	1126	  24.23400	-109.66700	31-Mar-03	
+JSL II 3457	 862	  40.29617	 -68.11133	26-Sep-03	Francesc Pages (pers.comm)