Student or educator? Sign up with your school email and get 6 months of Pro free.
CoChat
Sign Up
Cited by 10,905

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence

Open access
Lowe, Todd M., Eddy, Sean R.·1997·Nucleic Acids Research
DOI 10.1093/nar/25.5.955
Open this paper in CoChat — free account

Abstract

We describe a program, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Two previously described tRNA detection programs are used as fast, first-pass prefilters to identify candidate tRNAs, which are then analyzed by a highly selective tRNA covariance model. This work represents a practical application of RNA covariance models, which are general, probabilistic secondary structure profiles based on stochastic context-free grammars. tRNAscan-SE searches at approximately 30 000 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1093/nar/25.5.955

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Research works printed but not linked: 36

  1. Hatlen, 1971, J. Mol. Biol., 56, 535, 10.1016/0022-2836(71)90400-1 · DOI
  2. Oba, 1991, Proc. Nat. Acad. Sci. USA, 88, 921, 10.1073/pnas.88.3.921 · DOI
  3. Kanna, 1993, J. Mol. Biol., 230, 51, 10.1006/jmbi.1993.1125 · DOI
  4. Daniels, 1984, Nature, 317, 819, 10.1038/317819a0 · DOI
  5. Deininger, 1989, Mobile DNA, 619
  6. Dandekar, 1995, Trends Genet., 11, 45, 10.1016/S0168-9525(00)88996-9 · DOI
  7. Staden, 1980, Nucleic Acids Res., 8, 817, 10.1093/nar/8.16.3673 · DOI · Paper page
  8. Paolella, 1985, Comput. Appl. Biosci., 1, 149
  9. Shortridge, 1986, Comput. Appl. Biosci., 2, 13
  10. Marvel, 1986, Nucleic Acids Res., 14, 431, 10.1093/nar/14.1.431 · DOI
  11. Wozniak, 1990, Comput. Appl. Biosci., 6, 49
  12. Fichant, 1991, J. Mol. Biol., 220, 659, 10.1016/0022-2836(91)90108-I · DOI
  13. Pavesi, 1994, Nucleic Acids Res, 22, 1247, 10.1093/nar/22.7.1247 · DOI
  14. Altschul, 1990, J. Mol. Biol., 215, 403, 10.1016/S0022-2836(05)80360-2 · DOI · Paper page
  15. Pearson, 1988, Proc. Natl. Acad. Sci. USA, 85, 2444, 10.1073/pnas.85.8.2444 · DOI · Paper page
  16. Saurin, 1987, Comput. Appl. Biosci., 3, 115
  17. Staden, 1988, Comput. Appl. Biosci., 4, 53
  18. Gautheret, 1990, Comput. Appl. Biosci., 6, 325
  19. Sibbald, 1992, Comput. Appl. Biosci., 8, 45
  20. Laferrire, 1994, Comput. Appl. Biosci., 10, 211
  21. Billoud, 1996, Nucleic Acids Res., 24, 1395, 10.1093/nar/24.8.1395 · DOI
  22. Eddy, 1994, Nucleic Acids Res., 22, 2079, 10.1093/nar/22.11.2079 · DOI
  23. Grate, 1994, Proceedings Second International Conference on Intelligent Systems for Molecular Biology, 2, 138
  24. Sakakibara, 1994, Nucleic Acids Res., 22, 5112, 10.1093/nar/22.23.5112 · DOI · Paper page
  25. Gribskov, 1990, Methods Enzymol, 183, 146, 10.1016/0076-6879(90)83011-W · DOI · Paper page
  26. Krogh, 1994, J. Mol. Biol., 235, 1501, 10.1006/jmbi.1994.1104 · DOI
  27. Steinberg, 1993, Nucleic Acids Res, 21, 3011, 10.1093/nar/21.13.3011 · DOI
  28. Bernardi, 1993, Gene, 135, 57, 10.1016/0378-1119(93)90049-9 · DOI
  29. Green, 1993, J. Bacteriol, 175, 5091, 10.1128/JB.175.16.5091-5096.1993 · DOI
  30. Fraser, 1995, Science, 270, 397, 10.1126/science.270.5235.397 · DOI · Paper page
  31. Fleischmann, 1995, Science, 269, 496, 10.1126/science.7542800 · DOI
  32. Bult, 1996, Science, 273, 1058, 10.1126/science.273.5278.1058 · DOI · Paper page
  33. Boguski, 1993, Nature Genet, 4, 332, 10.1038/ng0893-332 · DOI · Paper page
  34. Westaway, 1995, tRNA: Structure, Biosynthesis and Function, 79, 10.1128/9781555818333.ch7 · DOI
  35. Keeney, 1995, Mol. Cell. Biol., 15, 217, 10.1128/MCB.15.1.217 · DOI
  36. Lisacek, 1994, J. Mol. Biol., 235, 1206, 10.1006/jmbi.1994.1074 · DOI

Cited by

See all 10,905

Metadata

Authors
Lowe, T. M., & Eddy, S. R.
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
1997-03-01
Volume
25
Issue
5
Pages
955-964
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/25.5.955
OpenAlex
W2149429041
Cited by
10,905
References
1
FWCI
10.24
Type
journal article
Language
en
Open access
green

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.