[Bioperl-l] Difference between

[tai kwan do]

Hello,

Maybe someone could help me out with this problem, I've tried to email ncbi 
about this but they didn't bother answering.  Basically, I'm seeing a 
difference in the data being output by stand-alone blast and online blast.  
The identities value are different between the xml output and the pairwise 
alignment output, even though I'm using the exact same input values.  The 
other difference I see is in the query and hit sequences.  I've included 
below the outputs using the same input parameters, is this normal behavior?

   gb|AE000111.1|AE000111 Escherichia coli K-12 MG1655 section 1 of 400 of 
the complete

         genome
        Length = 10596

Score =  589 bits (297), Expect = e-168
Identities = 315/324 (97%)
Strand = Plus / Plus


Query: 237 aggtaacggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgacagtg 296
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 237 aggtaacggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgacagtg 296


Query: 297 cgggcnnnnnnnnncgaccaaaggtaacgaggtaacaaccatgcgagtgttgaagttcgg 356
         |||||         ||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 297 cgggctttttttttcgaccaaaggtaacgaggtaacaaccatgcgagtgttgaagttcgg 356


Query: 357 cggtacatcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaa 416
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 357 cggtacatcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaa 416


Query: 417 tgccaggcaggggcaggtggccaccgtcctctctgcccccgccaaaatcaccaaccacct 476
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 417 tgccaggcaggggcaggtggccaccgtcctctctgcccccgccaaaatcaccaaccacct 476


Query: 477 ggtggcgatgattgaaaaaaccattagcggccaggatgctttacccaatatcagcgatgc 536
         ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 477 ggtggcgatgattgaaaaaaccattagcggccaggatgctttacccaatatcagcgatgc 536


Query: 537 cgaacgtatttttgccgaactttt 560
         ||||||||||||||||||||||||
Sbjct: 537 cgaacgtatttttgccgaactttt 560


      <Hit>
        <Hit_num>1</Hit_num>
        <Hit_id>gi|1786181|gb|AE000111.1|AE000111</Hit_id>
        <Hit_def>Escherichia coli K-12 MG1655 section 1 of 400 of the 
complete genome</Hit_def>
        <Hit_accession>AE000111</Hit_accession>
        <Hit_len>10596</Hit_len>
        <Hit_hsps>
          <Hsp>
            <Hsp_num>1</Hsp_num>
            <Hsp_bit-score>589.253</Hsp_bit-score>
            <Hsp_score>297</Hsp_score>
            <Hsp_evalue>1.04898e-168</Hsp_evalue>
            <Hsp_query-from>237</Hsp_query-from>
            <Hsp_query-to>560</Hsp_query-to>
            <Hsp_hit-from>237</Hsp_hit-from>
            <Hsp_hit-to>560</Hsp_hit-to>
            <Hsp_query-frame>1</Hsp_query-frame>
            <Hsp_hit-frame>1</Hsp_hit-frame>
            <Hsp_identity>324</Hsp_identity>
            <Hsp_positive>324</Hsp_positive>
            <Hsp_align-len>324</Hsp_align-len>
            
<Hsp_qseq>AGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT</Hsp_qseq>
            
<Hsp_hseq>AGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAGCCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAAGTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCCAGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTGAAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT</Hsp_hseq>
            
<Hsp_midline>||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||</Hsp_midline>
          </Hsp>
          <Hsp>

Thanks in advance

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