Input File Format

PHAST may accept and process either raw nucleotide sequence data in FASTA format or an annotated genome data in GenBank format. If the input file is in FASTA format, locus tags will be assigned sequentially for each identified CDS. Note that this is one FASTA file for the entire genome. We currently do not support annotated cDNAs in FASAT format. Please use the GenBank format for annotated genome. If the input file is in GenBank format, it must provide at least the CDS feature and the "/gene", "/locus_tag" and "/translation" tags inside the CDS features.

Raw Nucleotide Sequence Data Format

Example #1: This is an example of of a generic FASTA file. The entire file contains more than 5M nucleotides, and only the top portion is shown here. The header is not important for PHAST processing, though it will be displayed as the title of the genome.

>gi|16445223|ref|NC_002655.2| Escherichia coli O157:H7 str. EDL933 chromosome, complete genome
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTCTCTGACAGCAGC
TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC
ATTACCACCACCATCACCACCACCATCACCATTACCATTACCACAGGTAACGGTGCGGGCTGACGCGTAC
AGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTCGACCAAAGGTAACGAGGTAACA
ACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGGGTTGCCGATA
TTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCA
CCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGT
ATTTTTGCCGAACTTCTGACGGGACTCGCCGCCGCCCAGCCGGGATTCCCGCTGGCGCAATTGAAAACTT
TCGTCGACCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTAGGGCAGTGCCCGGA
TAGCATTAACGCTGCGCTGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAA
GCGCGCGGTCACAACGTTACCGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAAT
CTACTGTCGATATTGCAGAGTCCACCCGCCGTATTGCGGCAAGTCGTATTCCGGCTGATCACATGGTGCT
GATGGCAGGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTACTTGGACGCAACGGTTCCGACTAC
TCCGCGGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTAT
ATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAATCGATGTCCTACCAGGAAGCGATGGA
GCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGCACCATTACCCCCATCGCCCAGTTCCAGATCCCT
TGCCTGATTAAAAATACCGGAAATCCTCAAGCTCCAGGTACGCTCATTGGTGCCAGTCGTGATGAAGACG
AATTACCGGTCAAGGGCATTTCCAATCTGAATAATATGGCAATGTTCAGCGTTTCCGGCCCGGGGATGAA
AGGAATGGTCGGCATGGCGGCGCGCGTCTTTGCTGCAATGTCACGCGCCCGTATTTCCGTGGTGCTGATT
ACGCAATCATCTTCCGAATACAGTATCAGTTTCTGCGTTCCGCAAAGCGACTGTGTGCGAGCTGAACGGG
CAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAGCCGCTGGCGGTGACGGAACGGCT
GGCCATTATCTCGGTGGTAGGTGATGGTATGCGCACCTTGCGTGGGATCTCGGCGAAATTCTTTGCCGCG
CTGGCCCGCGCCAATATCAACATTGTCGCTATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGG
TAAATAACGATGATGCGACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTAT 
		

Example #2: Another example in FASTA format.

>unknown genome
AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTCTCTGACAGCAGC
TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC
ATTACCACCACCATCACCACCACCATCACCATTACCATTACCACAGGTAACGGTGCGGGCTGACGCGTAC
AGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTCGACCAAAGGTAACGAGGTAACA
ACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGGGTTGCCGATA
TTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCA
CCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGT
ATTTTTGCCGAACTTCTGACGGGACTCGCCGCCGCCCAGCCGGGATTCCCGCTGGCGCAATTGAAAACTT
TCGTCGACCAGGAATTTGCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTAGGGCAGTGCCCGGA
TAGCATTAACGCTGCGCTGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAA
GCGCGCGGTCACAACGTTACCGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAAT
CTACTGTCGATATTGCAGAGTCCACCCGCCGTATTGCGGCAAGTCGTATTCCGGCTGATCACATGGTGCT
GATGGCAGGTTTCACCGCCGGTAATGAAAAAGGCGAACTGGTGGTACTTGGACGCAACGGTTCCGACTAC
TCCGCGGCGGTGCTGGCTGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTAT
ATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAATCGATGTCCTACCAGGAAGCGATGGA
GCTTTCCTACTTCGGCGCTAAAGTTCTTCACCCCCGCACCATTACCCCCATCGCCCAGTTCCAGATCCCT
TGCCTGATTAAAAATACCGGAAATCCTCAAGCTCCAGGTACGCTCATTGGTGCCAGTCGTGATGAAGACG
AATTACCGGTCAAGGGCATTTCCAATCTGAATAATATGGCAATGTTCAGCGTTTCCGGCCCGGGGATGAA
AGGAATGGTCGGCATGGCGGCGCGCGTCTTTGCTGCAATGTCACGCGCCCGTATTTCCGTGGTGCTGATT
ACGCAATCATCTTCCGAATACAGTATCAGTTTCTGCGTTCCGCAAAGCGACTGTGTGCGAGCTGAACGGG
CAATGCAGGAAGAGTTCTACCTGGAACTGAAAGAAGGCTTACTGGAGCCGCTGGCGGTGACGGAACGGCT
GGCCATTATCTCGGTGGTAGGTGATGGTATGCGCACCTTGCGTGGGATCTCGGCGAAATTCTTTGCCGCG
CTGGCCCGCGCCAATATCAACATTGTCGCTATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGG
TAAATAACGATGATGCGACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTAT 
		

Annotated Genome Format

Example #1: This is an example of of a generic GenBank file. The entire file contains more than 20k lines, and only the header and first a few CDSs are shown here. Only the "LOCUS" and "DEFINITION" tags in the header are used and they are used for only for naming. All annotated genes must be recorded in the "FEATURES" section and associated with the "gene"and "CDS" sub-tags. The "CDS" portion may or may not have "/translation". " ORIGIN" tag and DNAsequence section must be in the file.

LOCUS       NC_002655            5528445 bp    DNA     circular BCT 14-DEC-2010
DEFINITION  Escherichia coli O157:H7 str. EDL933 chromosome, complete genome.
ACCESSION   NC_002655
VERSION     NC_002655.2  GI:16445223
DBLINK      Project: 57831
KEYWORDS    .
SOURCE      Escherichia coli O157:H7 str. EDL933
  ORGANISM  Escherichia coli O157:H7 str. EDL933
            Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5528445)
  AUTHORS   Perna,N.T., Plunkett,G. III, Burland,V., Mau,B., Glasner,J.D.,
            Rose,D.J., Mayhew,G.F., Evans,P.S., Gregor,J., Kirkpatrick,H.A.,
            Posfai,G., Hackett,J., Klink,S., Boutin,A., Shao,Y., Miller,L.,
            Grotbeck,E.J., Davis,N.W., Lim,A., Dimalanta,E., Potamousis,K.,
            Apodaca,J., Anantharaman,T.S., Lin,J., Yen,G., Schwartz,D.C.,
            Welch,R.A. and Blattner,F.R.
  TITLE     Genome sequence of enterohaemorrhagic Escherichia coli O157:H7
  JOURNAL   Nature 409 (6819), 529-533 (2001)
   PUBMED   11206551
REFERENCE   2  (bases 1 to 5528445)
  CONSRTM   NCBI Genome Project
  TITLE     Direct Submission
  JOURNAL   Submitted (28-SEP-2001) National Center for Biotechnology
            Information, NIH, Bethesda, MD 20894, USA
REFERENCE   3  (bases 1 to 5528445)
  AUTHORS   Perna,N.T., Plunkett,G. III, Burland,V., Mau,B., Glasner,J.D.,
            Rose,D.J., Mayhew,G.F., Evans,P.S., Gregor,J., Kirkpatrick,H.A.,
            Posfai,G., Hackett,J., Klink,S., Boutin,A., Shao,Y., Miller,L.,
            Grotbeck,E.J., Davis,N.W., Lim,A., Dimalanta,E., Potamousis,K.,
            Apodaca,J., Anantharaman,T.S., Lin,J., Yen,G., Schwartz,D.C.,
            Welch,R.A. and Blattner,F.R.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-OCT-2000) Laboratory of Genetics, University of
            Wisconsin, 445 Henry Mall, Madison, WI 53706, USA
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from AE005174.
            On Oct 26, 2001 this sequence version replaced gi:15799680.
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..5528445
                     /organism="Escherichia coli O157:H7 str. EDL933"
                     /mol_type="genomic DNA"
                     /strain="EDL933"
                     /serotype="O157:H7"
                     /db_xref="taxon:155864"
                     /note="enterohemorrhagic"
     gene            190..273
                     /gene="thrL"
                     /locus_tag="Z0001"
                     /db_xref="GeneID:962112"
     CDS             190..273
                     /gene="thrL"
                     /locus_tag="Z0001"
                     /function="leader; Amino acid biosynthesis: Threonine"
                     /note="involved in threonine biosynthesis; controls the
                     expression of the thrLABC operon"
                     /codon_start=1
                     /transl_table=11
                     /product="thr operon leader peptide"
                     /protein_id="NP_285693.1"
                     /db_xref="GI:15799681"
                     /db_xref="GeneID:962112"
                     /translation="MKRISTTITTTITTTITITITTGNGAG"
     gene            354..2816
                     /gene="thrA"
                     /locus_tag="Z0002"
                     /db_xref="GeneID:962110"
     CDS             354..2816
                     /gene="thrA"
                     /locus_tag="Z0002"
                     /EC_number="2.7.2.4"
                     /EC_number="1.1.1.13"
                     /function="enzyme; Amino acid biosynthesis: Threonine"
                     /note="multifunctional homotetrameric enzyme that
                     catalyzes the phosphorylation of aspartate to form
                     aspartyl-4-phosphate as well as conversion of aspartate
                     semialdehyde to homoserine; functions in a number of amino
                     acid biosynthetic pathways"
                     /codon_start=1
                     /transl_table=11
                     /product="bifunctional aspartokinase I/homeserine
                     dehydrogenase I"
                     /protein_id="NP_285694.1"
                     /db_xref="GI:15799682"
                     /db_xref="GeneID:962110"
                     /translation="MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKIT
                     NHLVAMIEKTISGQDALPNISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIK
                     HVLHGISLLGQCPDSINAALICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVGHY
                     LESTVDIAESTRRIAASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACL
                     RADCCEIWTDVDGVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQF
                     QIPCLIKNTGNPQAPGTLIGASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAAR
                     VFAAMSRARISVVLITQSSSEYSISFCVPQSDCVRAERAMQEEFYLELKEGLLEPLAV
                     TERLAIISVVGDGMRTLRGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATT
                     GVRVTHQMLFNTDQVIEVFVIGVGGVGGALLEQLKRQQSWLKNKHIDLRVCGVANSKA
                     LLTNVHGLNLENWQEELAQAKEPFNLGRLIRLVKEYHLLNPVIVDCTSSQAVADQYAD
                     FLREGFHVVTPNKKANTSSMDYYHLLRHAAEKSRRKFLYDTNVGAGLPVIENLQNLLN
                     AGDELMKFSGILSGSLSYIFGKLDEGMSFSEATTLAREMGYTEPDPRDDLSGMDVARK
                     LLILARETGRELELADIEIEPVLPAEFNAEGDVAAFMANLSQLDDLFAARVAKARDEG
                     KVLRYVGNIDEDGVCRVKIAEVDGNDPLFKVKNGENALAFYSHYYQPLPLVLRGYGAG
                     NDVTAAGVFADLLRTLSWKLGV"
     gene            2818..3750
                     /gene="thrB"
                     /locus_tag="Z0003"
                     /db_xref="GeneID:962111"
     CDS             2818..3750
                     /gene="thrB"
                     /locus_tag="Z0003"
                     /EC_number="2.7.1.39"
                     /function="enzyme; Amino acid biosynthesis: Threonine"
                     /note="catalyzes the formation of O-phospho-L-homoserine
                     from L-homoserine in threonine biosynthesis from asparate"
                     /codon_start=1
                     /transl_table=11
                     /product="homoserine kinase"
                     /protein_id="NP_285695.1"
                     /db_xref="GI:15799683"
                     /db_xref="GeneID:962111"
                     /translation="MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVESAETF
                     SLNNLGRFADKLPSEPRENIVYQCWERFCQELGKQIPVAMTLEKNMPIGSGLGSSACS
                     VVAALMAMNEHCGKPLNDTRLLALMGELEGRISGSIHYDNVAPCFLGGMQLMIEENDI
                     ISQQVPGFDEWLWVLAYPGIKVSTAEARAILPAQYRRQDCIAHGRHLAGFIHACYSRQ
                     PELAAKLMKDVIAEPYRERLLPGFRQARQAVAEIGAVASGISGSGPTLFALCDKPDTA
                     QRVADWLGKNYLQNQEGFVHICRLDTAGARVLEN"
     gene            3751..5037
                     /gene="thrC"
                     /locus_tag="Z0004"
                     /db_xref="GeneID:956660"
     CDS             3751..5037
                     /gene="thrC"
                     /locus_tag="Z0004"
                     /EC_number="4.2.3.1"
                     /function="enzyme; Amino acid biosynthesis: Threonine"
                     /note="catalyzes the formation of L-threonine from
                     O-phospho-L-homoserine"
                     /codon_start=1
                     /transl_table=11
                     /product="threonine synthase"
                     /protein_id="NP_285696.1"
                     /db_xref="GI:15799684"
                     /db_xref="GeneID:956660"
                     /translation="MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEID
                     EMLKLDFVTRSAKILSAFIGDEIPQEILEERVRAAFAFPAPVANVESDVGCLELFHGP
                     TLAFKDFGGRFMAQMLTHIAGDKPVTILTATSGDTGAAVAHAFYGLPNVKVVILYPRG
                     KISPLQEKLFCTLGGNIETVAIDGDFDACQALVKQAFDDEELKVALGLNSANSINISR
                     LLAQICYYFEAVAQLPQEARNQLVVSVPSGNFGDLTAGLLAKSLGLPVKRFIAATNVN
                     DTVPRFLHDGQWSPKATQATLSNAMDVSQPNNWPRVEELFRRKIWQLKELGYAAVDDE
                     TTQQTMRELKELGYTSEPHAAVAYRALRDQLNPGEYGLFLGTAHPAKFKESVEAILGE
                     TLDLPKELAERADLPLLSHNLPADFAALRKLMMNHQ"
     gene            5251..5547
                     /locus_tag="Z0005"
                     /db_xref="GeneID:956661"
     CDS             5251..5547
                     /locus_tag="Z0005"
                     /function="orf; Unknown function"
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="NP_285697.1"
                     /db_xref="GI:15799685"
                     /db_xref="GeneID:956661"
                     /translation="MKKMQSIVLALSLVLVAPMATQAAEITLVPSVKLQIGDRDNRGY
                     YWDGGHWRDHGWWKQHYEWRGNRWHPHGPPPPPRHHKKAHHDHHGGHGPGKHHR"
     gene            complement(5700..6476)
                     /gene="yaaA"
                     /locus_tag="Z0006"
                     /db_xref="GeneID:956662"
     CDS             complement(5700..6476)
                     /gene="yaaA"
                     /locus_tag="Z0006"
                     /function="orf; Unknown function"
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="NP_285698.1"
                     /db_xref="GI:15799686"
                     /db_xref="GeneID:956662"
                     /translation="MLILISPAKTLDYQSPLTTTRYTLPELLDNSQQLIHEARKLTPP
                     QISTLMRISDKLAGINAARFHDWQPDFTPENARQAILAFKGDVYTGLQAETFSEDDFD
                     FAQQHLRMLSGLYGVLRPLDLMQPYRLEMGIRLENARGKDLYQFWGDIITNKLNEALA
                     AQGDNVVINLASDEYFKSVKPKKLNAEIIKPVFLDEKNGKFKIISFYAKKARGLMSRF
                     IIENRLTKPEQLTGFNSEGYFFDEASSSNGELVFKRYEQR"
ORIGIN
	1 AAAACCCGGGTTT .......
       60 CCCGGGTTTAAAG .......
	......
//


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