LAST E-values
=============

It is useful to know whether alignments are significant, i.e. unlikely
to exist just by chance.  LAST indicates this by EG2 and E::

  a score=40 EG2=0.031 E=0.025
  s mouse.chrY  2905908 130 +  91744698 CAGTCAC---AAATTTCTATCAAATATAA--CAGCT...
  s human.chrX 57162275 127 + 156040895 CACTCACTGCAAATCCTTATCAAACGTAATTCAGCT...

  a score=40 EG2=0.031 E=0.0093
  s mouse.chrY  2905908 130 + 91744698 CAGTCAC---AAATTTCTATCAAATATAA--CAGCT...
  s human.chrY 24460641 127 + 57227415 CACTCACTGCAAATCCTTATCAAACGTAATTCAGCT...

**EG2** is "expected alignments per square giga".  This is the
expected number of alignments with greater or equal score, between two
randomly-shuffled sequences of length 1 billion each.

**E** is the expected number of alignments with greater or equal
score, between: a random sequence with the same length as the query
sequence, and a random sequence with the same length as the database.

In this example, the two alignments are identical, but their "E"
values are not.  That is because the query sequences have different
lengths: human.chrX is longer than human.chrY.

Default threshold
-----------------

By default, LAST reports alignments that are expected by chance at
most once per million query letters (for a given database).

Setting a threshold
-------------------

You can make lastal report alignments that are expected by chance at
most once per (say) thousand query letters, with option -D::

  lastal -D1000 humdb fuguMito.fa > myalns.maf

You can make lastal report alignments with EG2 ≤ (say) 10, with option
-E::

  lastal -E10 humdb fuguMito.fa > myalns.maf

Advanced issues
---------------

Letter frequencies
~~~~~~~~~~~~~~~~~~

LAST's E-values refer to randomly-shuffled sequences *with specific
letter frequencies*.  Those frequencies are determined by the
substitution score matrix.  You can see them by running lastal with
option -v (verbose).

If your sequences have very different letter frequencies (e.g. very
AT-rich DNA), the E-values will be misleading.  The best solution is
to use a suitable score matrix, such as AT77 or ATMAP.

For DNA-versus-protein alignment, however, only the protein
frequencies are determined by the score matrix.  The DNA frequencies
are fixed at 0.25.

Calculation of EG2
~~~~~~~~~~~~~~~~~~

EG2 is calculated from the score like this::

  EG2 = K * (1 billion) * (1 billion) * exp(-lambda * score)

The parameters lambda and K are printed in the header of lastal's
output.

Calculation of E
~~~~~~~~~~~~~~~~

E is calculated by this formula::

  E = K * area * exp(-lambda * score) * (number of strands)

This depends on the number of strands that are searched, either 1 or
2.

The area is approximately (database length) * (query length). However,
if the query (or database) is very short, this formula over-estimates
E.  LAST uses a "finite-size correction" to calculate E more
accurately.

Effect of option -D
~~~~~~~~~~~~~~~~~~~

Option -D indirectly sets the EG2 threshold, via this formula::

  1 = EG2 * (database length)/1e9 * (option -D)/1e9 * (number of strands)

Bit score
~~~~~~~~~

Some people like to use "bit scores".  If you are one of them, the bit
score can be calculated like this::

  Bit score = (lambda * score - ln[K]) / ln[2]
            = log2( 1e18 / EG2 )

Limitations
~~~~~~~~~~~

* E-values cannot be calculated for scoring schemes with weak mismatch
  or gap costs (e.g. match score = 99, mismatch cost = 1).  In such
  cases, lastal requires you to set a score threshold with option -e.

* There may be a long startup time to calculate the E-value parameters
  (lambda, K, and finite-size correction parameters), especially for
  alignment with frameshifts.  This is avoided, for particular scoring
  schemes, by storing the parameters in LAST's source code.
  Parameters for other scoring schemes can be added on request.  (Or
  you can do it yourself: run lastal with option -v, so it prints the
  E-value parameters, then copy them into LastEvaluer.cc.)

* The E-values do not account for lastal option -c.  If you use this
  option, the E-values will be under-estimates.

* The E-values are for local alignment.  So if you use lastal option
  -T1 (overlap alignment), the E-values will be over-estimates.

Other resources
~~~~~~~~~~~~~~~

For more flexible E-value calculation, try ALP and FALP:
http://www.ncbi.nlm.nih.gov/CBBresearch/Spouge/html_ncbi/html/index/software.html
