[Biopython-dev] [Bug 2530] Bio.Seq.translate() treats invalid codons as stops

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2530





------- Comment #9 from mmokrejs at ribosome.natur.cuni.cz  2008-07-19 12:40 EST -------
>gi|45741280|gb|CK993509.1|CK993509 024C12R1.2A ESTHcyl Hebeloma cylindrosporum cDNA clone ESTHcyl024C12, mRNA sequence
AAGAAAACGAGAAGGACGGGGTTATATAGTAAGGTACAAACAGGGCANNNNNNCCATTACACGACCAACT
TCTTCGCCTTGCCCTTTTTCTCAGAGTCCTTGTGCGACAGGAACTCGACCTCGGTCGCAAGAGGCCCAGC
AAGTCGCGCTCCCTCGGGGTACCCAAGCACACTCATCTTGAAATGCTTCCCAACTCCCTCAATCCTTTCC
CGCAGCCCCGCATCCTCCTCGGTCGGTGCAAGTCGCGTCCATATCGACAATCGATAAAACTGCGGCCGCG
TCGACACGATCACACCTGTAATCAGCGACGCAGACCCACTTCCACCCGTCAGCGTCGGCGATGGGTCAAA
TGTTTCCCCGATCGCAGCCAGCATCGTATACAGCCACATCTTGTCTACGTTGGGTCGGTTTTTATCTTTG
GGCAGTTGGATACTCCATTTTCCTCCAAGCTTGTTCGCCTCGTCCTCCCATGCGGGAATAATTCCCTCCT
TGAAAAGGTAATAATTTGCCTTCTGGGGCAGTTGAGATGGCGGTATGATGTTGTTATATAACCCCCAAAA
CTCCNNNNNGCTATCAAAGNNNNNGACCCGCNNNNNGTCCNCCANNNACCCTTNNNCCNNNNNANNNCCG
GNNNNNNNNNNNNTGNGGGTCNNNNNNNNNGCTNNNNNNNNNNTNNNNNG

resulted as of Aug 5 2007 in a six-frame translation

>gi|45741280|gb|CK993509.1|CK993509 gi|45741280|gb|CK993509.1|CK993509 024C12R1.2A ESTHcyl Hebeloma cylindrosporum cDNA clone ESTHcyl024C12, mRNA sequence frame:+1
KKTRRTGLYSKVQTG***HYTTNFFALPFFSESLCDRNSTSVARGPASRAPSGYPSTLILKCFPTPSILSRSPASSSVGASRVHIDNR*NCGRVDTITPVISDADPLPPVSVGDGSNVSPIAASIVYSHILSTLGRFLSLGSWILHFPPSLFASSSHAGIIPS
LKR**FAFWGS*DGGMMLLYNPQNS**LSK**TR**S***P*****P******V***A*****
>gi|45741280|gb|CK993509.1|CK993509 gi|45741280|gb|CK993509.1|CK993509 024C12R1.2A ESTHcyl Hebeloma cylindrosporum cDNA clone ESTHcyl024C12, mRNA sequence frame:+2
RKREGRGYIVRYKQG***ITRPTSSPCPFSQSPCATGTRPRSQEAQQVALPRGTQAHSS*NASQLPQSFPAAPHPPRSVQVASISTIDKTAAASTRSHL*SATQTHFHPSASAMGQMFPRSQPASYTATSCLRWVGFYLWAVGYSIFLQACSPRPPMRE*FPP
*KGNNLPSGAVEMAV*CCYITPKT***YQ***P****P*TL*****R*****G**********
>gi|45741280|gb|CK993509.1|CK993509 gi|45741280|gb|CK993509.1|CK993509 024C12R1.2A ESTHcyl Hebeloma cylindrosporum cDNA clone ESTHcyl024C12, mRNA sequence frame:+3
ENEKDGVI**GTNRA**PLHDQLLRLALFLRVLVRQELDLGRKRPSKSRSLGVPKHTHLEMLPNSLNPFPQPRILLGRCKSRPYRQSIKLRPRRHDHTCNQRRRPTSTRQRRRWVKCFPDRSQHRIQPHLVYVGSVFIFGQLDTPFSSKLVRLVLPCGNNSLLEKVIICLLGQLRWRYDVVI*PPKL**AIK**DP**V***P************G**********
>gi|45741280|gb|CK993509.1|CK993509 gi|45741280|gb|CK993509.1|CK993509 024C12R1.2A ESTHcyl Hebeloma cylindrosporum cDNA clone ESTHcyl024C12, mRNA sequence frame:-1
**********W************P***L**AQ**KLS**LKTPNILL*YGGRVDGVFRLIMEKFLP**GRTLLLRLFEPPFTS*VDGFLFLAGLHLFYTDICYDRR*PLCKLGSGCDCPPSPRRSD*CPH*HSCAGVKIANSYTCAERGWLLLRPDALS*LPQPFVKFYSHEPMGLPRAERPGERWLQLKDSVFLRLFFPFRFFNQHIT**TGQTWNDILGQEEQK
>gi|45741280|gb|CK993509.1|CK993509 gi|45741280|gb|CK993509.1|CK993509 024C12R1.2A ESTHcyl Hebeloma cylindrosporum cDNA clone ESTHcyl024C12, mRNA sequence frame:-2
**********G*****G*****FP*T****P***NY***SKPPIYCCSMAVELTGSSV**WKSSSLNKGVPSCSACSNLLLPHRLTGFYFWLGCICSTPTYATTDASPFVNWVAAATAHLHPDAATNVHTSTAAPASK*LTAIPALNVAGSSYAPTPFPNSLNPS*SSTHTNPWGSLALNDPENAGSSSRTACS*DSFSRSASSTSTL***RDKHGMIYWGRKSKR
>gi|45741280|gb|CK993509.1|CK993509 gi|45741280|gb|CK993509.1|CK993509 024C12R1.2A ESTHcyl Hebeloma cylindrosporum cDNA clone ESTHcyl024C12, mRNA sequence frame:-3
*****S***L******A*****S***P**RP**ETI**PQNPQYIVVVWR*S*RGLPFNNGKVPPLIRAYPPAPLVRTSFYLIG*RVSIFGWVASVLHRHMLRPTLAPL*TG*RLRLPTFTQTQRLMSTLAQLRRRQNS*QLYLR*TWLAPPTPRRPFLTPSTLRKVLLTRTHGAPSR*TTRRTLAPAQGQRVPETLFPVPLLQPAHY***GTNME*YIGAGRAKE


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