Detailed papers on LAST
=======================

LAST has many ingredients, some of which are described in these
papers.  If you find an ingredient useful, please cite the
corresponding paper.  Citation is important because it provides
feedback on which research work was useful, and helps to justify the
research to society.

1. `Adaptive seeds tame genomic sequence comparison`__.  Kiełbasa SM,
   Wan R, Sato K, Horton P, Frith MC.  Genome Res. 2011 21(3):487-93.

   __ http://genome.cshlp.org/content/21/3/487.long

   This describes the main algorithms used by LAST.

2. `Incorporating sequence quality data into alignment improves DNA
   read mapping`__.  Frith MC, Wan R, Horton P.  Nucleic Acids
   Res. 2010 38(7):e100.

   __ http://nar.oxfordjournals.org/content/38/7/e100.long

   How LAST uses sequence quality data.

3. `Parameters for Accurate Genome Alignment`__.  Frith MC, Hamada M,
   Horton P.  BMC Bioinformatics. 2010 11:80.

   __ http://www.biomedcentral.com/1471-2105/11/80

   Choice of score parameters, ambiguity of alignment columns, and
   gamma-centroid alignment.

4. `A new repeat-masking method enables specific detection of
   homologous sequences`__.  Frith MC.  Nucleic Acids Res. 2011
   39(4):e23.

   __ http://nar.oxfordjournals.org/content/39/4/e23.long

   This describes the tantan algorithm for finding simple /
   low-complexity / tandem repeats, which reliably prevents
   non-homologous alignments, unlike other repeat finders.

5. `Gentle masking of low-complexity sequences improves homology
   search`__.  Frith MC.  PLoS One. 2011 6(12):e28819.

   __ http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0028819

   This describes what LAST does with repeats after they have been
   found.

6. `Probabilistic alignments with quality scores: an application to
   short-read mapping toward accurate SNP/indel detection`__.  Hamada
   M, Wijaya E, Frith MC, Asai K.  Bioinformatics. 2011
   27(22):3085-92.

   __ http://bioinformatics.oxfordjournals.org/content/27/22/3085.long

   Describes probabilistic alignment using sequence quality data, and
   LAMA alignment.

7. `A mostly traditional approach improves alignment of
   bisulfite-converted DNA`__.  Frith MC, Mori R, Asai K.  Nucleic
   Acids Res. 2012 40(13):e100.

   __ http://nar.oxfordjournals.org/content/40/13/e100.long

   This describes alignment of bisulfite-converted DNA, and an update
   for use of fastq quality data that allows for non-uniform base
   frequencies.

8. `An approximate Bayesian approach for mapping paired-end DNA reads
   to a reference genome`__.  Shrestha AM, Frith MC.
   Bioinformatics. 2013 29(8):965-72.

   __ http://bioinformatics.oxfordjournals.org/content/29/8/965.long

   This describes the algorithm used by ``last-pair-probs``.

9. `Improved search heuristics find 20,000 new alignments between
   human and mouse genomes`__.  Frith MC, Noé L.  Nucleic Acids
   Res. 2014 42(7):e59.

   __ http://nar.oxfordjournals.org/content/42/7/e59.long

   This describes sensitive DNA seeding (MAM8 and MAM4).

10. `Frameshift alignment: statistics and post-genomic
    applications`__.  Sheetlin SL, Park Y, Frith MC, Spouge JL.
    Bioinformatics. 2014 30(24):3575-82.

    __ http://bioinformatics.oxfordjournals.org/content/30/24/3575.long

    Describes "old-style" DNA-versus-protein alignment allowing for
    frameshifts (without ``last-train``).

11. `Split-alignment of genomes finds orthologies more accurately`__.
    Frith MC, Kawaguchi R.  Genome Biology. 2015 16:106.

    __ http://www.genomebiology.com/content/16/1/106

    Describes the split alignment algorithm, and its application to
    whole genome alignment.

12. `Training alignment parameters for arbitrary sequencers with
    LAST-TRAIN`__.  Hamada M, Ono Y, Asai K Frith MC.
    Bioinformatics. 2017 33(6):926-928.

    __ https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btw742

    Describes ``last-train``.

13. `A Simplified Description of Child Tables for Sequence Similarity
    Search`__.  Frith MC, Shrestha A.  IEEE/ACM Trans Comput Biol
    Bioinform. 2018.

    __ https://ieeexplore.ieee.org/document/8288582/

    Describes how LAST uses child tables.

14. `Minimally-overlapping words for sequence similarity search`__.
    Frith MC, Noé L, Kucherov G.  Bioinformatics. 2020

    __ https://doi.org/10.1093/bioinformatics/btaa1054

    Describes the ``lastdb -u RY`` sparsity options, for LAST version < 1407.

15. `Improved DNA-versus-protein homology search for protein fossils`__.
    Yao Y, Frith MC.  IEEE/ACM Trans Comput Biol Bioinform. 2022

    __ https://doi.org/10.1109/TCBB.2022.3177855

    Describes "new-style" DNA-versus-protein search with
    ``last-train --codon``.

16. `How to optimally sample a sequence for rapid analysis`__.
    Frith MC, Shaw J, Spouge JL.

    __ https://doi.org/10.1101/2022.08.18.504476

    Describes the ``lastdb -u RY`` sparsity options, for LAST version >= 1407.

External methods
----------------

LAST of course owes its ideas to much previous research.  Here are
listed only implementations that are directly used in LAST.

* `The Gumbel pre-factor k for gapped local alignment can be estimated
  from simulations of global alignment`__.  Sheetlin S, Park Y, Spouge
  JL.  Nucleic Acids Res. 2005 33(15):4987-94.

  __ http://nar.oxfordjournals.org/content/33/15/4987.long

  Describes how E-values are calculated.

* `New finite-size correction for local alignment score
  distributions`__.  Park Y, Sheetlin S, Ma N, Madden TL, Spouge JL.
  BMC Res Notes. 2012 5:286.

  __ http://www.biomedcentral.com/1756-0500/5/286

  Describes a correction that makes the E-values more accurate for
  short sequences.

* `GNU Parallel - The Command-Line Power Tool`__.  Tange O.  ;login:
  The USENIX Magazine. 2011:42-47.

  __ https://www.usenix.org/publications/login/february-2011-volume-36-number-1/gnu-parallel-command-line-power-tool

  It seems traditional not to cite this kind of ingredient, which is
  unfortunate because the same reasons for citation apply.
