Gapped BLAST and PSI-BLAST: A New Generation of Protein Database Search Programs
Nucleic Acids Research, 1997 · paper · Biomedicine
Describes refinements to BLAST protein searching: a two-hit extension rule and gapped alignments give about threefold speed, and PSI-BLAST iteratively builds position-specific score matrices to detect weak similarities, illustrated by new BRCT superfamily members.
Checked: PDF from europepmc.org, fetched 5 Oct 2026. Page numbers are those of that PDF.
0 findings
None that passed a second check.
9 minor (typos and the like; most checked by the judge only)
Substance The Figure 2 legend gives 'nominal score 45, or 23.6 bits, calculated using λu and Ku', and p.4 repeats '23.6 bits (calculated using λu and Ku)'. With the stated λu = 0.3176 and Ku = 0.134, a score of 45 converts to 23.52 bits, i.e. 23.5.
- p. 3 Figure 2 legend
yields an HSP with nominal score 45, or 23.6 bits, calculated using λu and Ku
- p. 3 Text, two-hit section
λu = 0.3176 and Ku = 0.134
- p. 4 Text, right column
produces an HSP with score 23.6 bits (calculated using λu and Ku)
- p. 3 Figure 2 legend
an HSP with nominal score 45, or 23.6 bits, calculated using λu and Ku
Only the authors can say what is right here.
Judge's note: Computed (λS − ln K)/ln 2 with ln 0.134 = −2.00992 and ln 2 = 0.693147. Score 45: (14.292 + 2.00992)/0.693147 = 23.52 bits. The same parameters reproduce the Figure 1 legend's range: score 37 gives 19.85 (printed 19.9) and score 92 gives 45.05 (printed 45.1). That makes the 23.6 the inconsistent value. The difference is 0.1 bit; only the authors can say whether different internal parameters were used.
Second check: another model agreed
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Wording Figure 6 legend: 'A χ2 goodness-of-fit test with 34 degrees of freedom has value 41.8, corresponding to a P-value of 0.20'. The statistic and the P value do not correspond under the declared test: the upper tail of χ2(34) at 41.8 is about 0.17. The p.8 text ('lower than one would expect 20% of the time') is ambiguous in the same way.
- p. 9 Figure 6 legend
freedom has value 41.8, corresponding to a P-value of 0.20
- p. 8 Text, right column
which is lower than one would expect 20% of the time
- p. 8 BLAST applied to position-specific score matrices, text
has value 41.8, which is lower than one would expect 20% of the time
- p. 9 Figure 6 legend
A χ2 goodness-of-fit test with 34 degrees of freedom has value 41.8, corresponding to a P-value of 0.20.
Only the authors can say what is right here.
Judge's note: Both places state 34 degrees of freedom. I checked with the Wilson–Hilferty approximation: (41.8/34)^(1/3) = 1.0713, mean 1 − 2/306 = 0.99346, SD 0.0808, giving z ≈ 0.96 and an upper tail of about 0.17. The 80th percentile of χ2(34), interpolated from tables, is about 40.7, which is below 41.8. Nothing in the paper says the df or the P value were adjusted. The p.8 sentence 'lower than one would expect 20% of the time' reads as a claim that 41.8 is below the 80th percentile, which conflicts with the same calculation. This is put to the authors as a query.
Second check: another model agreed
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Wording p.9, right column: 'The mean numbers of shuffled database sequences with E-values <1 and 10' uses a strict inequality, whereas the left column ('yielding E-values ≤1 and 10') and the Table 2 headers use ≤.
- p. 9 Text, right column
numbers of shuffled database sequences with E-values <1 and 10
- p. 9 Text, left column / Table 2 headers
yielding E-values ≤1 and 10
Judge's note: The page 9 crops show '<1' in the right column and '≤1' in the left-column sentence that describes the same Table 2 counts. This is a minor inconsistency in how the threshold is stated, and it is immaterial for continuous E-values.
Second check: another model agreed
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Wording Table 4 gives the organism for TDT (GenBank 2149634) as 'Mus domestica', which is not a recognised binomial.
- p. 12 Table 4, TDT row
Mus domestica
Only the authors can say what is right here.
Judge's note: Rests on outside knowledge: that 'Mus domestica' is not a valid species name; candidates include Monodelphis domestica and Mus musculus/domesticus. The page 12 crop shows 'Mus domestica' in italics. Elsewhere the table uses standard binomials. The intended organism cannot be determined from the files, so only the authors can say what is right.
Second check: another model agreed
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Typo Introduction, p.1: 'the conjunction of several new algorithmic ideas allow a new version of BLAST' has a singular subject ('conjunction') with a plural verb; it should read 'allows'.
- p. 1 Introduction, 2nd paragraph (right column)
conjunction of several new algorithmic ideas allow a new version
- p. 1 Introduction
the conjunction of several new algorithmic ideas allow a new version
Judge's note: The page 1 crop shows the wording exactly as quoted. The head noun is 'conjunction', so the verb should be 'allows'. This is a cosmetic grammar error.
Second check: none (judge only)
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Typo p.7, Sequence weights: 'we shall henceforth mean its weighted rather its raw frequencies' is missing 'than' ('weighted rather than its raw frequencies').
- p. 7 Sequence weights, end of first paragraph
weighted rather its raw frequencies
- p. 7
mean its weighted rather its raw frequencies
Judge's note: The page 7 crop shows the wording as printed, so this is not an extraction artefact.
Second check: none (judge only)
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Typo p.10: 'the gapped BLAST program runs on average three times faster then the original' should read 'than'.
- p. 10 Performance evaluation text, left column
three times faster then the original
- p. 10 Performance evaluation, para after Table 3
runs on average three times faster then the original
Judge's note: The full page 10 image shows 'faster then the original' in the left column.
Second check: none (judge only)
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Typo Reference 61 lists the co-author as 'Druck,T., Croche,C.M. and Huebner,K.'; the name is probably Croce,C.M.
- p. 14 Reference 61
Croche,C.M. and Huebner,K.
- p. 14 Reference 61
Druck,T., Croche,C.M. and Huebner,K.
Only the authors can say what is right here.
Judge's note: Rests on outside knowledge: that the co-author of Ohta et al. (1996) Cell 84:587 is Carlo M. Croce. The page 14 image shows 'Croche,C.M.', so this is not an extraction error.
Second check: none (judge only)
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Typo Reference 30 gives the first author as 'Schneider,T.S.'; the initials are probably T.D. (Thomas D. Schneider).
- p. 14 Reference 30
Schneider,T.S., Stormo,G.D., Gold,L. and Ehrenfeucht,A. (1986)
Only the authors can say what is right here.
Judge's note: Rests on outside knowledge: that the 1986 J. Mol. Biol. 188:415–431 paper is by Thomas D. Schneider. The page 14 image shows 'Schneider,T.S.' as printed.
Second check: none (judge only)