ó ÊIc@sLddlZddlZddlmZddlmZddlmZmZdfd„ƒYZ de fd„ƒYZ d e fd „ƒYZ e d krHdd l m Z d ZdZdZdGHdGHe ƒZx"eje eƒƒD] ZeGHqäWe ƒZx1eje eƒddddfƒD] ZeGHq!We ƒZx9eje edeƒddddfƒD] ZeGHqfWHdGHdGHe ƒZxAeje eƒdeƒD]$ZejGejGejGHejGHq¥We ƒZxAeje eƒdeƒD]$ZejGejGejGHejGHqòWe ƒZxAeje eƒdeƒD]$ZejGejGejGHejGHq?We ƒZxAeje eƒdeƒD]$ZejGejGejGHejGHqŒWHdGHdGHe ƒZx"eje eƒƒD] ZeGHqÞWHdGHdGHe ƒZxAeje eƒdeƒD]$ZejGejGejGHejGHqWndS(iÿÿÿÿN(tSeq(t SeqRecord(tgeneric_alphabettgeneric_proteint InsdcScannercBsÝeZdZdZdZdgZdgZdZdZdgZ dd„Z d„Z d „Z d „Z ed „Zd „Zd „Zd„Zd„Zd„Zd„Zed„Zed„Zed„Zedd„ZRS(s¤Basic functions for breaking up a GenBank/EMBL file into sub sections. The International Nucleotide Sequence Database Collaboration (INSDC) between the DDBJ, EMBL, and GenBank. These organisations all use the same "Feature Table" layout in their plain text flat file formats. However, the header and sequence sections of an EMBL file are very different in layout to those produced by GenBank/DDBJ.tXXXisXXX***FEATURES***XXXsXXX***END FEATURES***XXXitcCs~t|jƒ|jkst‚x)|jD]}||jƒks(t‚q(Wt|jƒ|jksht‚||_d|_ dS(N( tlent RECORD_STARTt HEADER_WIDTHtAssertionErrortSEQUENCE_HEADERStrstriptFEATURE_QUALIFIER_SPACERtFEATURE_QUALIFIER_INDENTtdebugtNonetline(tselfRtmarker((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GenBank/Scanner.pyt__init__4s  cCs||_d|_dS(NR(thandleR(RR((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GenBank/Scanner.pyt set_handle<s cCs xútrü|jr'|j}d|_n|jjƒ}|sQ|jrMdGHnd S||j |jkr†|jdkr‚d|GHnPn|jƒ}|dkr¸|jdkrùdGHqùq|dkrÞ|jdkrùdGHqùq|jdkrd|GHqqW||_|S( s°Read in lines until find the ID/LOCUS line, which is returned. Any preamble (such as the header used by the NCBI on *.seq.gz archives) will we ignored.Rs End of fileisFound the start of a record: s//s&Skipping // marking end of last records!Skipping blank line before records$Skipping header line before record: N( tTrueRRtreadlineRRR RR (RR((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GenBank/Scanner.pyt find_start@s0            cCsò|j|j |jks%tdƒ‚g}x·trä|jjƒ}|sXtdƒ‚n|jƒ}||j krˆ|j r„dGHnPn||j jƒ|j kr¹|j rµdGHnPn|dkrÔtdƒ‚n|j |ƒq.W||_|S(s˜Return list of strings making up the header New line characters are removed. Assumes you have just read in the ID/LOCUS line. sNot at start of records*Premature end of line during sequence datasFound header tablesFound start of sequences//s0Premature end of sequence data marker '//' found( RR RR RRRt ValueErrorR tFEATURE_START_MARKERSRR tappend(Rt header_linesR((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GenBank/Scanner.pyt parse_header]s*       cCs@|jjƒ|jkr-|jr)dGHngSx.|jjƒ|jkr]|jjƒ|_q0Wg}|j}xÃtr2|s‹tdƒ‚n||j jƒ|j kr¼|jr¸dGHnPn|jƒ}|dkrãtdƒ‚n||j kr|jrdGHn|jjƒ}Pn|d|j !j ƒdkrEtd |ƒ‚n|r‰|jjƒ}xÒ||j |j kr…|jjƒ}q]Wqp|d|j !j ƒ}||j g}|jjƒ}xU||j |j ksé|jƒdkr|j||j jƒƒ|jjƒ}qÁW|j|j||ƒƒqpW||_|S( s›Return list of tuples for the features (if present) Each feature is returned as a tuple (key, location, qualifiers) where key and location are strings (e.g. "CDS" and "complement(join(490883..490885,1..879))") while qualifiers is a list of two string tuples (feature qualifier keys and values). Assumes you have already read to the start of the features table. sDidn't find any feature tables+Premature end of line during features tablesFound start of sequences//s2Premature end of features table, marker '//' foundsFound end of featuresiRs)Expected a feature qualifier in line '%s'(RR RRRRRRR R tFEATURE_END_MARKERSRtstripR Rt parse_feature(RtskiptfeaturesRt feature_keyt feature_lines((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GenBank/Scanner.pytparse_features|sN         c Cs$ttd |ƒƒ}yØ|jƒ}|jƒ}x*|ddkr\||jƒjƒ7}q3Wg}xy|D]q}|ddkr‰|jdƒ}|d|!}||d} |dkrÖ|d}|j|d fƒqÛ| ddkrs| ddks| dkr0xX| ddkr,| d|jƒ7} qWn-| dksBt‚|jr]d || fGHn|j|| fƒqÛ|j|| fƒqjt |ƒdks¡t‚||ddks»t‚||ddd|f|d6       $ cCs|j|jkrwxb|j|j jƒ|jkrs|jjƒ|_|js^tdƒ‚n|jjƒ|_qWn|j|j jƒ|jks¢tdƒ‚xJt rî|jjƒ}|sÏtdƒ‚n|jƒ}|dkr¥Pq¥q¥W||_gdfS(sGreturns a tuple containing a list of any misc strings, and the sequencesPremature end of filesNot at start of sequences*Premature end of line during sequence datas//R( RRR R R RRRR R(RR((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GenBank/Scanner.pyt parse_footers"" "     cCsdS(sÕHandle the LOCUS/ID line, passing data to the comsumer This should be implemented by the EMBL / GenBank specific subclass Used by the parse_records() and parse() methods. N((RtconsumerR((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GenBank/Scanner.pyt_feed_first_line,scCsdS(sæHandle the header lines (list of strings), passing data to the comsumer This should be implemented by the EMBL / GenBank specific subclass Used by the parse_records() and parse() methods. N((RR9R1((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GenBank/Scanner.pyt_feed_header_lines5scCs‘|jƒx€|D]x\}}}|j|ƒ|j|ƒxL|D]D\}}|j|gƒ|dk rA|j|jddƒƒqAqAWqWdS(s’Handle the feature table (list of tuples), passing data to the comsumer Used by the parse_records() and parse() methods. s t N(tstart_feature_tableR$tlocationtfeature_qualifier_nameRtfeature_qualifier_descriptiontreplace(RR9tfeature_tuplesR$tlocation_stringR4tq_keytq_value((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GenBank/Scanner.pyt_feed_feature_table?s    cCsdS(sýHandle any lines between features and sequence (list of strings), passing data to the consumer This should be implemented by the EMBL / GenBank specific subclass Used by the parse_records() and parse() methods. N((RR9R1((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GenBank/Scanner.pyt_feed_misc_linesMscCsÙ|j|ƒ|jƒs&d|_tS|j||jƒ|j||jƒƒ|rt|j ||j dtƒƒn|j dt ƒ|j ƒ\}}|j ||ƒ|j|ƒ|jdƒ|jdksÕt‚t S(sæFeed a set of data into the consumer. This method is intended for use with the "old" code in Bio.GenBank Arguments: handle - A handle with the information to parse. consumer - The consumer that should be informed of events. do_features - Boolean, should the features be parsed? Skipping the features can be much faster. Return values: true - Passed a record false - Did not find a record R"s//N(RRRtdatatFalseR:RR;RRFR&RR8RGtsequencet record_endR (RRR9t do_featurest misc_linestsequence_string((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GenBank/Scanner.pytfeedVs     cCsYddlm}ddlm}|ddd|ƒƒ}|j||ƒrQ|jSdSdS(sReturns a SeqRecord (with SeqFeatures if do_features=True) See also the method parse_records() for use on multi-record files. iÿÿÿÿ(t_FeatureConsumer(tFeatureValueCleanert use_fuzzinessitfeature_cleanerN(t Bio.GenBankRPtBio.GenBank.utilsRQRORHR(RRRLRPRQR9((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GenBank/Scanner.pytparseˆs  ccstxmtro|j|ƒ}|dkr(Pn|jdk s=t‚|jdksRt‚|jdksgt‚|VqWdS(sReturns a SeqRecord object iterator Each record (from the ID/LOCUS line to the // line) becomes a SeqRecord The SeqRecord objects include SeqFeatures if do_features=True This method is intended for use in Bio.SeqIO ssN(RRVRtidR tnamet description(RRRLtrecord((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GenBank/Scanner.pyt parse_records™s  t protein_idt locus_tagtproductc csw|j|ƒxc|jƒrr|jƒ|jƒ}x7trk|jjƒ}|sTPn|d dkr5Pq5q5W|jƒ|_xñ|D]é\}}}|dkr‚t ddƒ} | j } |j ddƒ| d|ƒ‚||d(!}x+|jd ƒd!krM|jd dƒ}q#W|jdƒ}t|ƒd"kstd#|ƒ‚t|ƒd$ks¡td%|ƒ‚|j|dƒ|j|d$ƒ|d)d0!jƒdkr|d(d)!dkr|j d?|d0d5!jƒƒn|j |d)d5!jƒƒ|j |dd7!ƒ|j |dd@!ƒnã||jƒj dƒdkr¸||jƒdkr¤|j||jƒƒq8t jdA|IJn€t|jƒƒdBkr(|jƒdCdOkr(|j|jƒd$ƒ|j|jƒd"ƒt jdF|IJntdG|ƒ‚dS(PNR<is LOCUS s%LOCUS line does not start correctly: ii!s bp s aa s rc s=LOCUS line does not contain size units at expected position: i)i*s2LOCUS line does not contain space at position 42: i3RtlineartcircularsALOCUS line does not contain valid entry (linear, circular, ...): i4s2LOCUS line does not contain space at position 52: i7i>s s;LOCUS line does not contain spaces from position 56 to 62: i@iAR¡s6LOCUS line does not contain - at position 65 in date: iDiEs6LOCUS line does not contain - at position 69 in date: s iÿÿÿÿis4Cannot parse the name and length in the LOCUS line: is+Name and length collide in the LOCUS line: tPROTEINiIi(i,i/s sss-sds-sms-sCLOCUS line does not have valid strand type (Single stranded, ...): i6tDNAtRNAsALOCUS line does not contain valid sequence type (DNA, RNA, ...): s2LOCUS line does not contain space at position 55: i?s2LOCUS line does not contain space at position 64: iCs2LOCUS line does not contain space at position 68: iFiGs6LOCUS line does not contain - at position 71 in date: iJiKs6LOCUS line does not contain - at position 75 in date: sPROTEIN iOs5Warning: Minimal LOCUS line found - is this correct? iitaatbps7Warning: Malformed LOCUS line found - is this correct? s)Did not recognise the LOCUS line layout: (s bp s aa s rc (s bp s aa s rc (RR¸R¹(s bp s aa s rc (s bp s aa s rc (s sss-sds-sms-(RR¸R¹(R½R¾(R R R R.RARuRR}RŠR~RtdateRytsyststderrR(RR9RtGENBANK_INDENTtGENBANK_SPACERtname_and_length_strtname_and_length((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GenBank/Scanner.pyR: sž             ,  "%          ,!.c Cs˜|j}d|}idd6dd6dd6dd 6d d 6d d 6dd6dd6dd6dd6dd6dd6dd6dd6dd6d d!6d"d#6}td|ƒ}|jd$ƒt|ƒ}y¼|jƒ}x©trr|sÚPn|| jƒ}||jƒ} |d%kr×x+| jd&ƒd'kr3| j d&dƒ} q W| jd(ƒd'krY|j | ƒno|j r”d)| j d(ƒd*d+| j d(ƒd,d-GHn|j | j d(ƒd*ƒ|j | j d(ƒd,ƒ|jƒ}qÊ|d.kr^|j d,krd/| d-GHn| jƒ} x[trk|jƒ}|| |krg| d||7} |j d,krhd0| d-GHqhqPqWx+| jd&ƒd'kr™| j d&dƒ} qoW| jdƒd'krÞ|j d1krÎd2| d3GHn|j| ƒqo|j d1kr#d2| | jdƒ d4| | jdƒd,d3GHn|j| | jdƒ ƒ|j| | jdƒd,ƒqÊ|d5kr7| } d$} xlträ|jƒ}|d*|!|krà| s°d6|krÅ| d||7} qá| d||jƒ7} qyPqyW|j| ƒ| jƒd$kr|j d,krd7GHn|j| jƒƒ~ ~ qÊ|d8kræ|j d,krZd9GHng} | j| ƒxctrÒ|jƒ}|d*|!|krÎ||} | j| ƒ|j d1krÏd:| d-GHqÏqpPqpW|j| ƒ~ qÊ||krNxztrJ|jƒ}|d*|!|kr/| d||7} qõt|||ƒ| ƒPqõWqÊ|j rcd;|GHn|jƒ}qÊWWntk r“td<ƒ‚nXdS(=NR<Rt DEFINITIONR„t ACCESSIONtnidtNIDtpidtPIDt db_sourcetDBSOURCEtkeywordstKEYWORDStsegmenttSEGMENTtsourcetSOURCER‘tAUTHORStconsrtmtCONSRTMtprojecttPROJECTtdblinktDBLINKR“tTITLER•tJOURNALt medline_idtMEDLINERªR¥tremarktREMARKRtVERSIONs iÿÿÿÿs GI:s Version [is], gi [iRŸt REFERENCEsFound reference [sExtended reference text [isReference number "s"s", "tORGANISMRxs!Taxonomy line(s) missing or blanktCOMMENTs Found commentsComment continuation [sIgnoring GenBank header line: sProblem in header(R R,RRR+R-RR R.RARŽRRutgiR§R¨R—R™R›R«R/R( RR9R1RÂRÃR®R¯RR°RHt organism_datat lineage_datat comment_list((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GenBank/Scanner.pyR;´sÎ         2    6!    !              cCs|j}d|}|jdƒt|ƒ}y¾x³|D]«}|jdƒdkr|djƒ}|r|jr|d|GHn|j|ƒqn|jdƒdkrâ|djƒ}|râ|jrÏd |GHn|j|ƒqân|jd ƒdkr|d jƒ}|j|ƒn|jd ƒdkrL|djƒ}|j |ƒn|jd ƒdkr6|djƒ}|}xWt rÐ|j ƒ}|s–Pqz|| |kr½|||j ƒ7}qzt d|ƒ‚qzW|j|ƒq6q6WdSWntk r t dƒ‚nXdS(NR<Rs BASE COUNTii s base_count = R´isorigin_name = sWGS it WGS_SCAFLDR³s(Expected CONTIG continuation line, got: s%Problem in misc lines before sequence(R RR+R.R Rt base_countt origin_nametwgstadd_wgs_scafldRR-R Rtcontig_locationR/(RR9R1RÂRÃR¯RRî((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GenBank/Scanner.pyRGNsL          (RlRmRnRR RRRR R R8R:R;RG(((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GenBank/Scanner.pyR±Õs   + © št__main__(tStringIOs,)LOCUS SCU49845 5028 bp DNA PLN 21-JUN-1999 DEFINITION Saccharomyces cerevisiae TCP1-beta gene, partial cds, and Axl2p (AXL2) and Rev7p (REV7) genes, complete cds. ACCESSION U49845 VERSION U49845.1 GI:1293613 KEYWORDS . SOURCE Saccharomyces cerevisiae (baker's yeast) ORGANISM Saccharomyces cerevisiae Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces. REFERENCE 1 (bases 1 to 5028) AUTHORS Torpey,L.E., Gibbs,P.E., Nelson,J. and Lawrence,C.W. TITLE Cloning and sequence of REV7, a gene whose function is required for DNA damage-induced mutagenesis in Saccharomyces cerevisiae JOURNAL Yeast 10 (11), 1503-1509 (1994) PUBMED 7871890 REFERENCE 2 (bases 1 to 5028) AUTHORS Roemer,T., Madden,K., Chang,J. and Snyder,M. TITLE Selection of axial growth sites in yeast requires Axl2p, a novel plasma membrane glycoprotein JOURNAL Genes Dev. 10 (7), 777-793 (1996) PUBMED 8846915 REFERENCE 3 (bases 1 to 5028) AUTHORS Roemer,T. TITLE Direct Submission JOURNAL Submitted (22-FEB-1996) Terry Roemer, Biology, Yale University, New Haven, CT, USA FEATURES Location/Qualifiers source 1..5028 /organism="Saccharomyces cerevisiae" /db_xref="taxon:4932" /chromosome="IX" /map="9" CDS <1..206 /codon_start=3 /product="TCP1-beta" /protein_id="AAA98665.1" /db_xref="GI:1293614" /translation="SSIYNGISTSGLDLNNGTIADMRQLGIVESYKLKRAVVSSASEA AEVLLRVDNIIRARPRTANRQHM" gene 687..3158 /gene="AXL2" CDS 687..3158 /gene="AXL2" /note="plasma membrane glycoprotein" /codon_start=1 /function="required for axial budding pattern of S. cerevisiae" /product="Axl2p" /protein_id="AAA98666.1" /db_xref="GI:1293615" /translation="MTQLQISLLLTATISLLHLVVATPYEAYPIGKQYPPVARVNESF TFQISNDTYKSSVDKTAQITYNCFDLPSWLSFDSSSRTFSGEPSSDLLSDANTTLYFN VILEGTDSADSTSLNNTYQFVVTNRPSISLSSDFNLLALLKNYGYTNGKNALKLDPNE VFNVTFDRSMFTNEESIVSYYGRSQLYNAPLPNWLFFDSGELKFTGTAPVINSAIAPE TSYSFVIIATDIEGFSAVEVEFELVIGAHQLTTSIQNSLIINVTDTGNVSYDLPLNYV YLDDDPISSDKLGSINLLDAPDWVALDNATISGSVPDELLGKNSNPANFSVSIYDTYG DVIYFNFEVVSTTDLFAISSLPNINATRGEWFSYYFLPSQFTDYVNTNVSLEFTNSSQ DHDWVKFQSSNLTLAGEVPKNFDKLSLGLKANQGSQSQELYFNIIGMDSKITHSNHSA NATSTRSSHHSTSTSSYTSSTYTAKISSTSAAATSSAPAALPAANKTSSHNKKAVAIA CGVAIPLGVILVALICFLIFWRRRRENPDDENLPHAISGPDLNNPANKPNQENATPLN NPFDDDASSYDDTSIARRLAALNTLKLDNHSATESDISSVDEKRDSLSGMNTYNDQFQ SQSKEELLAKPPVQPPESPFFDPQNRSSSVYMDSEPAVNKSWRYTGNLSPVSDIVRDS YGSQKTVDTEKLFDLEAPEKEKRTSRDVTMSSLDPWNSNISPSPVRKSVTPSPYNVTK HRNRHLQNIQDSQSGKNGITPTTMSTSSSDDFVPVKDGENFCWVHSMEPDRRPSKKRL VDFSNKSNVNVGQVKDIHGRIPEML" gene complement(3300..4037) /gene="REV7" CDS complement(3300..4037) /gene="REV7" /codon_start=1 /product="Rev7p" /protein_id="AAA98667.1" /db_xref="GI:1293616" /translation="MNRWVEKWLRVYLKCYINLILFYRNVYPPQSFDYTTYQSFNLPQ FVPINRHPALIDYIEELILDVLSKLTHVYRFSICIINKKNDLCIEKYVLDFSELQHVD KDDQIITETEVFDEFRSSLNSLIMHLEKLPKVNDDTITFEAVINAIELELGHKLDRNR RVDSLEEKAEIERDSNWVKCQEDENLPDNNGFQPPKIKLTSLVGSDVGPLIIHQFSEK LISGDDKILNGVYSQYEEGESIFGSLF" ORIGIN 1 gatcctccat atacaacggt atctccacct caggtttaga tctcaacaac ggaaccattg 61 ccgacatgag acagttaggt atcgtcgaga gttacaagct aaaacgagca gtagtcagct 121 ctgcatctga agccgctgaa gttctactaa gggtggataa catcatccgt gcaagaccaa 181 gaaccgccaa tagacaacat atgtaacata tttaggatat acctcgaaaa taataaaccg 241 ccacactgtc attattataa ttagaaacag aacgcaaaaa ttatccacta tataattcaa 301 agacgcgaaa aaaaaagaac aacgcgtcat agaacttttg gcaattcgcg tcacaaataa 361 attttggcaa cttatgtttc ctcttcgagc agtactcgag ccctgtctca agaatgtaat 421 aatacccatc gtaggtatgg ttaaagatag catctccaca acctcaaagc tccttgccga 481 gagtcgccct cctttgtcga gtaattttca cttttcatat gagaacttat tttcttattc 541 tttactctca catcctgtag tgattgacac tgcaacagcc accatcacta gaagaacaga 601 acaattactt aatagaaaaa ttatatcttc ctcgaaacga tttcctgctt ccaacatcta 661 cgtatatcaa gaagcattca cttaccatga cacagcttca gatttcatta ttgctgacag 721 ctactatatc actactccat ctagtagtgg ccacgcccta tgaggcatat cctatcggaa 781 aacaataccc cccagtggca agagtcaatg aatcgtttac atttcaaatt tccaatgata 841 cctataaatc gtctgtagac aagacagctc aaataacata caattgcttc gacttaccga 901 gctggctttc gtttgactct agttctagaa cgttctcagg tgaaccttct tctgacttac 961 tatctgatgc gaacaccacg ttgtatttca atgtaatact cgagggtacg gactctgccg 1021 acagcacgtc tttgaacaat acataccaat ttgttgttac aaaccgtcca tccatctcgc 1081 tatcgtcaga tttcaatcta ttggcgttgt taaaaaacta tggttatact aacggcaaaa 1141 acgctctgaa actagatcct aatgaagtct tcaacgtgac ttttgaccgt tcaatgttca 1201 ctaacgaaga atccattgtg tcgtattacg gacgttctca gttgtataat gcgccgttac 1261 ccaattggct gttcttcgat tctggcgagt tgaagtttac tgggacggca ccggtgataa 1321 actcggcgat tgctccagaa acaagctaca gttttgtcat catcgctaca gacattgaag 1381 gattttctgc cgttgaggta gaattcgaat tagtcatcgg ggctcaccag ttaactacct 1441 ctattcaaaa tagtttgata atcaacgtta ctgacacagg taacgtttca tatgacttac 1501 ctctaaacta tgtttatctc gatgacgatc ctatttcttc tgataaattg ggttctataa 1561 acttattgga tgctccagac tgggtggcat tagataatgc taccatttcc gggtctgtcc 1621 cagatgaatt actcggtaag aactccaatc ctgccaattt ttctgtgtcc atttatgata 1681 cttatggtga tgtgatttat ttcaacttcg aagttgtctc cacaacggat ttgtttgcca 1741 ttagttctct tcccaatatt aacgctacaa ggggtgaatg gttctcctac tattttttgc 1801 cttctcagtt tacagactac gtgaatacaa acgtttcatt agagtttact aattcaagcc 1861 aagaccatga ctgggtgaaa ttccaatcat ctaatttaac attagctgga gaagtgccca 1921 agaatttcga caagctttca ttaggtttga aagcgaacca aggttcacaa tctcaagagc 1981 tatattttaa catcattggc atggattcaa agataactca ctcaaaccac agtgcgaatg 2041 caacgtccac aagaagttct caccactcca cctcaacaag ttcttacaca tcttctactt 2101 acactgcaaa aatttcttct acctccgctg ctgctacttc ttctgctcca gcagcgctgc 2161 cagcagccaa taaaacttca tctcacaata aaaaagcagt agcaattgcg tgcggtgttg 2221 ctatcccatt aggcgttatc ctagtagctc tcatttgctt cctaatattc tggagacgca 2281 gaagggaaaa tccagacgat gaaaacttac cgcatgctat tagtggacct gatttgaata 2341 atcctgcaaa taaaccaaat caagaaaacg ctacaccttt gaacaacccc tttgatgatg 2401 atgcttcctc gtacgatgat acttcaatag caagaagatt ggctgctttg aacactttga 2461 aattggataa ccactctgcc actgaatctg atatttccag cgtggatgaa aagagagatt 2521 ctctatcagg tatgaataca tacaatgatc agttccaatc ccaaagtaaa gaagaattat 2581 tagcaaaacc cccagtacag cctccagaga gcccgttctt tgacccacag aataggtctt 2641 cttctgtgta tatggatagt gaaccagcag taaataaatc ctggcgatat actggcaacc 2701 tgtcaccagt ctctgatatt gtcagagaca gttacggatc acaaaaaact gttgatacag 2761 aaaaactttt cgatttagaa gcaccagaga aggaaaaacg tacgtcaagg gatgtcacta 2821 tgtcttcact ggacccttgg aacagcaata ttagcccttc tcccgtaaga aaatcagtaa 2881 caccatcacc atataacgta acgaagcatc gtaaccgcca cttacaaaat attcaagact 2941 ctcaaagcgg taaaaacgga atcactccca caacaatgtc aacttcatct tctgacgatt 3001 ttgttccggt taaagatggt gaaaattttt gctgggtcca tagcatggaa ccagacagaa 3061 gaccaagtaa gaaaaggtta gtagattttt caaataagag taatgtcaat gttggtcaag 3121 ttaaggacat tcacggacgc atcccagaaa tgctgtgatt atacgcaacg atattttgct 3181 taattttatt ttcctgtttt attttttatt agtggtttac agatacccta tattttattt 3241 agtttttata cttagagaca tttaatttta attccattct tcaaatttca tttttgcact 3301 taaaacaaag atccaaaaat gctctcgccc tcttcatatt gagaatacac tccattcaaa 3361 attttgtcgt caccgctgat taatttttca ctaaactgat gaataatcaa aggccccacg 3421 tcagaaccga ctaaagaagt gagttttatt ttaggaggtt gaaaaccatt attgtctggt 3481 aaattttcat cttcttgaca tttaacccag tttgaatccc tttcaatttc tgctttttcc 3541 tccaaactat cgaccctcct gtttctgtcc aacttatgtc ctagttccaa ttcgatcgca 3601 ttaataactg cttcaaatgt tattgtgtca tcgttgactt taggtaattt ctccaaatgc 3661 ataatcaaac tatttaagga agatcggaat tcgtcgaaca cttcagtttc cgtaatgatc 3721 tgatcgtctt tatccacatg ttgtaattca ctaaaatcta aaacgtattt ttcaatgcat 3781 aaatcgttct ttttattaat aatgcagatg gaaaatctgt aaacgtgcgt taatttagaa 3841 agaacatcca gtataagttc ttctatatag tcaattaaag caggatgcct attaatggga 3901 acgaactgcg gcaagttgaa tgactggtaa gtagtgtagt cgaatgactg aggtgggtat 3961 acatttctat aaaataaaat caaattaatg tagcatttta agtataccct cagccacttc 4021 tctacccatc tattcataaa gctgacgcaa cgattactat tttttttttc ttcttggatc 4081 tcagtcgtcg caaaaacgta taccttcttt ttccgacctt ttttttagct ttctggaaaa 4141 gtttatatta gttaaacagg gtctagtctt agtgtgaaag ctagtggttt cgattgactg 4201 atattaagaa agtggaaatt aaattagtag tgtagacgta tatgcatatg tatttctcgc 4261 ctgtttatgt ttctacgtac ttttgattta tagcaagggg aaaagaaata catactattt 4321 tttggtaaag gtgaaagcat aatgtaaaag ctagaataaa atggacgaaa taaagagagg 4381 cttagttcat cttttttcca aaaagcaccc aatgataata actaaaatga aaaggatttg 4441 ccatctgtca gcaacatcag ttgtgtgagc aataataaaa tcatcacctc cgttgccttt 4501 agcgcgtttg tcgtttgtat cttccgtaat tttagtctta tcaatgggaa tcataaattt 4561 tccaatgaat tagcaatttc gtccaattct ttttgagctt cttcatattt gctttggaat 4621 tcttcgcact tcttttccca ttcatctctt tcttcttcca aagcaacgat ccttctaccc 4681 atttgctcag agttcaaatc ggcctctttc agtttatcca ttgcttcctt cagtttggct 4741 tcactgtctt ctagctgttg ttctagatcc tggtttttct tggtgtagtt ctcattatta 4801 gatctcaagt tattggagtc ttcagccaat tgctttgtat cagacaattg actctctaac 4861 ttctccactt cactgtcgag ttgctcgttt ttagcggaca aagatttaat ctcgttttct 4921 ttttcagtgt tagattgctc taattctttg agctgttctc tcagctcctc atatttttct 4981 tgccatgact cagattctaa ttttaagcta ttcaatttct ctttgatc //sŸLOCUS AAD51968 143 aa linear BCT 21-AUG-2001 DEFINITION transcriptional regulator RovA [Yersinia enterocolitica]. ACCESSION AAD51968 VERSION AAD51968.1 GI:5805369 DBSOURCE locus AF171097 accession AF171097.1 KEYWORDS . SOURCE Yersinia enterocolitica ORGANISM Yersinia enterocolitica Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Yersinia. REFERENCE 1 (residues 1 to 143) AUTHORS Revell,P.A. and Miller,V.L. TITLE A chromosomally encoded regulator is required for expression of the Yersinia enterocolitica inv gene and for virulence JOURNAL Mol. Microbiol. 35 (3), 677-685 (2000) MEDLINE 20138369 PUBMED 10672189 REFERENCE 2 (residues 1 to 143) AUTHORS Revell,P.A. and Miller,V.L. TITLE Direct Submission JOURNAL Submitted (22-JUL-1999) Molecular Microbiology, Washington University School of Medicine, Campus Box 8230, 660 South Euclid, St. Louis, MO 63110, USA COMMENT Method: conceptual translation. FEATURES Location/Qualifiers source 1..143 /organism="Yersinia enterocolitica" /mol_type="unassigned DNA" /strain="JB580v" /serotype="O:8" /db_xref="taxon:630" Protein 1..143 /product="transcriptional regulator RovA" /name="regulates inv expression" CDS 1..143 /gene="rovA" /coded_by="AF171097.1:380..811" /note="regulator of virulence" /transl_table=11 ORIGIN 1 mestlgsdla rlvrvwrali dhrlkplelt qthwvtlhni nrlppeqsqi qlakaigieq 61 pslvrtldql eekglitrht candrrakri klteqsspii eqvdgvicst rkeilggisp 121 deiellsgli dklerniiql qsk // sUID X56734; SV 1; linear; mRNA; STD; PLN; 1859 BP. XX AC X56734; S46826; XX DT 12-SEP-1991 (Rel. 29, Created) DT 25-NOV-2005 (Rel. 85, Last updated, Version 11) XX DE Trifolium repens mRNA for non-cyanogenic beta-glucosidase XX KW beta-glucosidase. XX OS Trifolium repens (white clover) OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; OC eurosids I; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium. XX RN [5] RP 1-1859 RX PUBMED; 1907511. RA Oxtoby E., Dunn M.A., Pancoro A., Hughes M.A.; RT "Nucleotide and derived amino acid sequence of the cyanogenic RT beta-glucosidase (linamarase) from white clover (Trifolium repens L.)"; RL Plant Mol. Biol. 17(2):209-219(1991). XX RN [6] RP 1-1859 RA Hughes M.A.; RT ; RL Submitted (19-NOV-1990) to the EMBL/GenBank/DDBJ databases. RL Hughes M.A., University of Newcastle Upon Tyne, Medical School, Newcastle RL Upon Tyne, NE2 4HH, UK XX FH Key Location/Qualifiers FH FT source 1..1859 FT /organism="Trifolium repens" FT /mol_type="mRNA" FT /clone_lib="lambda gt10" FT /clone="TRE361" FT /tissue_type="leaves" FT /db_xref="taxon:3899" FT CDS 14..1495 FT /product="beta-glucosidase" FT /EC_number="3.2.1.21" FT /note="non-cyanogenic" FT /db_xref="GOA:P26204" FT /db_xref="InterPro:IPR001360" FT /db_xref="InterPro:IPR013781" FT /db_xref="UniProtKB/Swiss-Prot:P26204" FT /protein_id="CAA40058.1" FT /translation="MDFIVAIFALFVISSFTITSTNAVEASTLLDIGNLSRSSFPRGFI FT FGAGSSAYQFEGAVNEGGRGPSIWDTFTHKYPEKIRDGSNADITVDQYHRYKEDVGIMK FT DQNMDSYRFSISWPRILPKGKLSGGINHEGIKYYNNLINELLANGIQPFVTLFHWDLPQ FT VLEDEYGGFLNSGVINDFRDYTDLCFKEFGDRVRYWSTLNEPWVFSNSGYALGTNAPGR FT CSASNVAKPGDSGTGPYIVTHNQILAHAEAVHVYKTKYQAYQKGKIGITLVSNWLMPLD FT DNSIPDIKAAERSLDFQFGLFMEQLTTGDYSKSMRRIVKNRLPKFSKFESSLVNGSFDF FT IGINYYSSSYISNAPSHGNAKPSYSTNPMTNISFEKHGIPLGPRAASIWIYVYPYMFIQ FT EDFEIFCYILKINITILQFSITENGMNEFNDATLPVEEALLNTYRIDYYYRHLYYIRSA FT IRAGSNVKGFYAWSFLDCNEWFAGFTVRFGLNFVD" FT mRNA 1..1859 FT /experiment="experimental evidence, no additional details FT recorded" XX SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other; aaacaaacca aatatggatt ttattgtagc catatttgct ctgtttgtta ttagctcatt 60 cacaattact tccacaaatg cagttgaagc ttctactctt cttgacatag gtaacctgag 120 tcggagcagt tttcctcgtg gcttcatctt tggtgctgga tcttcagcat accaatttga 180 aggtgcagta aacgaaggcg gtagaggacc aagtatttgg gataccttca cccataaata 240 tccagaaaaa ataagggatg gaagcaatgc agacatcacg gttgaccaat atcaccgcta 300 caaggaagat gttgggatta tgaaggatca aaatatggat tcgtatagat tctcaatctc 360 ttggccaaga atactcccaa agggaaagtt gagcggaggc ataaatcacg aaggaatcaa 420 atattacaac aaccttatca acgaactatt ggctaacggt atacaaccat ttgtaactct 480 ttttcattgg gatcttcccc aagtcttaga agatgagtat ggtggtttct taaactccgg 540 tgtaataaat gattttcgag actatacgga tctttgcttc aaggaatttg gagatagagt 600 gaggtattgg agtactctaa atgagccatg ggtgtttagc aattctggat atgcactagg 660 aacaaatgca ccaggtcgat gttcggcctc caacgtggcc aagcctggtg attctggaac 720 aggaccttat atagttacac acaatcaaat tcttgctcat gcagaagctg tacatgtgta 780 taagactaaa taccaggcat atcaaaaggg aaagataggc ataacgttgg tatctaactg 840 gttaatgcca cttgatgata atagcatacc agatataaag gctgccgaga gatcacttga 900 cttccaattt ggattgttta tggaacaatt aacaacagga gattattcta agagcatgcg 960 gcgtatagtt aaaaaccgat tacctaagtt ctcaaaattc gaatcaagcc tagtgaatgg 1020 ttcatttgat tttattggta taaactatta ctcttctagt tatattagca atgccccttc 1080 acatggcaat gccaaaccca gttactcaac aaatcctatg accaatattt catttgaaaa 1140 acatgggata cccttaggtc caagggctgc ttcaatttgg atatatgttt atccatatat 1200 gtttatccaa gaggacttcg agatcttttg ttacatatta aaaataaata taacaatcct 1260 gcaattttca atcactgaaa atggtatgaa tgaattcaac gatgcaacac ttccagtaga 1320 agaagctctt ttgaatactt acagaattga ttactattac cgtcacttat actacattcg 1380 ttctgcaatc agggctggct caaatgtgaa gggtttttac gcatggtcat ttttggactg 1440 taatgaatgg tttgcaggct ttactgttcg ttttggatta aactttgtag attagaaaga 1500 tggattaaaa aggtacccta agctttctgc ccaatggtac aagaactttc tcaaaagaaa 1560 ctagctagta ttattaaaag aactttgtag tagattacag tacatcgttt gaagttgagt 1620 tggtgcacct aattaaataa aagaggttac tcttaacata tttttaggcc attcgttgtg 1680 aagttgttag gctgttattt ctattatact atgttgtagt aataagtgca ttgttgtacc 1740 agaagctatg atcataacta taggttgatc cttcatgtat cagtttgatg ttgagaatac 1800 tttgaattaa aagtcttttt ttattttttt aaaaaaaaaa aaaaaaaaaa aaaaaaaaa 1859 // sGenBank CDS Iterations=====================RhtgeneR]R^s sGenBank Iterations=================RLsEMBL CDS Iterations==================sEMBL Iterations==============(RÀR¶tBio.SeqRt Bio.SeqRecordRt Bio.AlphabetRRRRoR±RlRðt gbk_examplet gbk_example2t embl_exampletgRkRZR[RIRWRXRYR`Rte(((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/GenBank/Scanner.pytsv  ÿÚÛÿ£ §1b       "  "  "  "    "