Seqanswers Leaderboard Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts
  • fungs
    Member
    • Jan 2010
    • 10

    Blast raw score calculation

    Hello,

    I know this sounds strange but I am having problems to validate the BLAST raw alignment scores (not the bit scores). Here an example alignment:

    -------------------------------------------------------

    Query: 100009 (Length=100)

    Hit: NZ_ABBZ01004690 gi|153879981|ref|NZ_ABBZ01004690.1| Beggiatoa sp. PS, whole genome shotgun sequence
    Length=280

    Score = 176 bits (194), Expected = 6e-42
    Identities = 99/100 (99%), Gaps = 0/100 (0%)
    Strand=Plus/Minus

    TCTGTTCTGTTCCATTGATCTATATCTCTGTTTTGGTACCAGTACCATGCTGTTTTGGTTACTGTAGCCTTGTAGTATAGTTTGAAGTCAGGTAGCGTGA
    ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||
    TCTGTTCTGTTCCATTGATCTATATCTCTGTTTTGGTACCAGTACCATGCTGTTTTGGTTACTGTAGCCTTGTAGTATAGTTTGAAGTCAGGTAGTGTGA

    -------------------------------------------------------

    My scoring matrix is:
    match: 2
    mismatch: -3
    gap open: 5
    gap extension: 2

    Following the formula from the NCBI web site http://www.ncbi.nlm.nih.gov/Educatio...t_Scores2.html (and what other aligners produce as raw score) this makes

    99*2 - 3 = 195 and not 194 like BLAST says:

    <Hsp_num>1</Hsp_num>
    <Hsp_bit-score>176.213077892943</Hsp_bit-score>
    <Hsp_score>194</Hsp_score>
    <Hsp_evalue>6.28580662796915e-42</Hsp_evalue>
    <Hsp_query-from>1</Hsp_query-from>
    <Hsp_query-to>100</Hsp_query-to>
    <Hsp_hit-from>108</Hsp_hit-from>
    <Hsp_hit-to>9</Hsp_hit-to>
    <Hsp_query-frame>1</Hsp_query-frame>
    <Hsp_hit-frame>-1</Hsp_hit-frame>
    <Hsp_identity>99</Hsp_identity>
    <Hsp_positive>99</Hsp_positive>
    <Hsp_gaps>0</Hsp_gaps>
    <Hsp_align-len>100</Hsp_align-len>

    In fact I noticed that all BLAST raw scores are even! I am using BLAST version 2.2.22+. Do I miss an import point here?
  • robs
    Senior Member
    • May 2010
    • 116

    #2
    Did you try to use BLAST+ instead? If the problem does occur with BLAST+, I would switch. You might also want to update to the latest BLAST version.

    Comment

    • fungs
      Member
      • Jan 2010
      • 10

      #3
      Yes, I am using BLAST+. I am currently running the latest version to see whether it makes any difference. Anyhow, this shoudn't be if it is really a bug. I couldn't find anything about it in the change logs from 2.2.22+ to 2.2.24+ so I rather think that it will give the same results with the latest version. What do you mean by "you should switch"?

      Comment

      • robs
        Senior Member
        • May 2010
        • 116

        #4
        If the raw score is a huge issue for you, you might want to consider alternative alignment programs (switch to an alternative program).
        You could also try to write the NCBI people who wrote the BLAST+ paper.

        Comment

        • fungs
          Member
          • Jan 2010
          • 10

          #5
          Yes thanks, I counterchecked with the latest BLAST+ version and found the same issue. The raw score is important to me because when I compare different aligners using the same scoring scheme should result in more or less the same alignments with the same raw scores.

          Another point is that BLAST bit scores are calculated from the raw scores. This would mean that also the bit scores are slightly wrong!

          I will write them an email, unfortunately they don't have a developers mailing list at the NCBI...

          Comment

          • fungs
            Member
            • Jan 2010
            • 10

            #6
            Just to let you know: Here is some evidence on the issue. I checked different versions and engines of NCBI BLAST. This seems to be an optimization in the code that is on purpose. The effect is that raw score can differ up to 3 points from real score.

            blast2.2.24+:

            * * * <Parameters_expect>10000</Parameters_expect>
            * * * <Parameters_sc-match>2</Parameters_sc-match>
            * * * <Parameters_sc-mismatch>-3</Parameters_sc-mismatch>
            * * * <Parameters_gap-open>5</Parameters_gap-open>
            * * * <Parameters_gap-extend>2</Parameters_gap-extend>
            * * * <Parameters_filter>F</Parameters_filter>

            * * * * * * * <Hsp_num>1</Hsp_num>
            * * * * * * * <Hsp_bit-score>176.213077892943</Hsp_bit-score>
            * * * * * * * <Hsp_score>194</Hsp_score>
            * * * * * * * <Hsp_evalue>6.28580662796915e-42</Hsp_evalue>
            * * * * * * * <Hsp_query-from>1</Hsp_query-from>
            * * * * * * * <Hsp_query-to>100</Hsp_query-to>
            * * * * * * * <Hsp_hit-from>108</Hsp_hit-from>
            * * * * * * * <Hsp_hit-to>9</Hsp_hit-to>
            * * * * * * * <Hsp_query-frame>1</Hsp_query-frame>
            * * * * * * * <Hsp_hit-frame>-1</Hsp_hit-frame>
            * * * * * * * <Hsp_identity>99</Hsp_identity>
            * * * * * * * <Hsp_positive>99</Hsp_positive>
            * * * * * * * <Hsp_gaps>0</Hsp_gaps>
            * * * * * * * <Hsp_align-len>100</Hsp_align-len>
            * * * * * * *
            <Hsp_qseq>TCTGTTCTGTTCCATTGATCTATATCTCTGTTTTGGTACCAGTACCATGCTGTTTTGGTTACTGTAGCCTTGTAGTATAGTTTGAAGTCAGGTAGCGTGA</Hsp_qseq>
            * * * * * * *
            <Hsp_hseq>TCTGTTCTGTTCCATTGATCTATATCTCTGTTTTGGTACCAGTACCATGCTGTTTTGGTTACTGTAGCCTTGTAGTATAGTTTGAAGTCAGGTAGTGTGA</Hsp_hseq>
            * * * * * * *
            <Hsp_midline>||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||
            </Hsp_midline>

            ================================================================================
            blast2.2.24:

            * * * <Parameters_expect>10000</Parameters_expect>
            * * * <Parameters_sc-match>2</Parameters_sc-match>
            * * * <Parameters_sc-mismatch>-3</Parameters_sc-mismatch>
            * * * <Parameters_gap-open>5</Parameters_gap-open>
            * * * <Parameters_gap-extend>2</Parameters_gap-extend>
            * * * <Parameters_filter>F</Parameters_filter>

            * * * * * * * <Hsp_num>1</Hsp_num>
            * * * * * * * <Hsp_bit-score>176.213</Hsp_bit-score>
            * * * * * * * <Hsp_score>194</Hsp_score>
            * * * * * * * <Hsp_evalue>6.28581e-42</Hsp_evalue>
            * * * * * * * <Hsp_query-from>100</Hsp_query-from>
            * * * * * * * <Hsp_query-to>1</Hsp_query-to>
            * * * * * * * <Hsp_hit-from>9</Hsp_hit-from>
            * * * * * * * <Hsp_hit-to>108</Hsp_hit-to>
            * * * * * * * <Hsp_query-frame>1</Hsp_query-frame>
            * * * * * * * <Hsp_hit-frame>-1</Hsp_hit-frame>
            * * * * * * * <Hsp_identity>99</Hsp_identity>
            * * * * * * * <Hsp_positive>99</Hsp_positive>
            * * * * * * * <Hsp_align-len>100</Hsp_align-len>
            * * * * * * *
            <Hsp_qseq>TCACGCTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAATGGAACAGAACAGA</Hsp_qseq>
            * * * * * * *
            <Hsp_hseq>TCACACTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAATGGAACAGAACAGA</Hsp_hseq>
            * * * * * * *
            <Hsp_midline>|||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
            </Hsp_midline>

            ================================================================================

            blast2.2.24-legacy:

            * * * <Parameters_expect>10000</Parameters_expect>
            * * * <Parameters_sc-match>2</Parameters_sc-match>
            * * * <Parameters_sc-mismatch>-3</Parameters_sc-mismatch>
            * * * <Parameters_gap-open>5</Parameters_gap-open>
            * * * <Parameters_gap-extend>2</Parameters_gap-extend>
            * * * <Parameters_filter>F</Parameters_filter>

            * * * * * * * <Hsp_num>1</Hsp_num>
            * * * * * * * <Hsp_bit-score>177.115</Hsp_bit-score>
            * * * * * * * <Hsp_score>195</Hsp_score>
            * * * * * * * <Hsp_evalue>3.36455e-42</Hsp_evalue>
            * * * * * * * <Hsp_query-from>100</Hsp_query-from>
            * * * * * * * <Hsp_query-to>1</Hsp_query-to>
            * * * * * * * <Hsp_hit-from>9</Hsp_hit-from>
            * * * * * * * <Hsp_hit-to>108</Hsp_hit-to>
            * * * * * * * <Hsp_query-frame>1</Hsp_query-frame>
            * * * * * * * <Hsp_hit-frame>-1</Hsp_hit-frame>
            * * * * * * * <Hsp_identity>99</Hsp_identity>
            * * * * * * * <Hsp_positive>99</Hsp_positive>
            * * * * * * * <Hsp_align-len>100</Hsp_align-len>
            * * * * * * *
            <Hsp_qseq>TCACGCTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAATGGAACAGAACAGA</Hsp_qseq>
            * * * * * * *
            <Hsp_hseq>TCACACTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGTACTGGTACCAAAACAGAGATATAGATCAATGGAACAGAACAGA</Hsp_hseq>
            * * * * * * *
            <Hsp_midline>|||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
            </Hsp_midline>

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Pathogen Surveillance with Advanced Genomic Tools
              by seqadmin




              The COVID-19 pandemic highlighted the need for proactive pathogen surveillance systems. As ongoing threats like avian influenza and newly emerging infections continue to pose risks, researchers are working to improve how quickly and accurately pathogens can be identified and tracked. In a recent SEQanswers webinar, two experts discussed how next-generation sequencing (NGS) and machine learning are shaping efforts to monitor viral variation and trace the origins of infectious...
              03-24-2025, 11:48 AM
            • seqadmin
              New Genomics Tools and Methods Shared at AGBT 2025
              by seqadmin


              This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.

              The Headliner
              The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...
              03-03-2025, 01:39 PM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 03-20-2025, 05:03 AM
            0 responses
            49 views
            0 reactions
            Last Post seqadmin  
            Started by seqadmin, 03-19-2025, 07:27 AM
            0 responses
            57 views
            0 reactions
            Last Post seqadmin  
            Started by seqadmin, 03-18-2025, 12:50 PM
            0 responses
            50 views
            0 reactions
            Last Post seqadmin  
            Started by seqadmin, 03-03-2025, 01:15 PM
            0 responses
            201 views
            0 reactions
            Last Post seqadmin  
            Working...