# LAST seeding schemes

LAST's critical first step is to find seeds, i.e. initial matches between query and reference sequences. It can use various seeding schemes, which allow different kinds of mismatches at different seed positions.

Note

A seeding scheme consists of a seed alphabet, such as:

    1  A C G T
    0  ACGT
    T  AG CT

and one or more patterns, such as this one:

    1T1T10T1101101

Each symbol in a pattern represents a grouping of sequence letters: in this example, `T` represents the grouping `AG CT`. At each position in an initial match, mismatches are allowed between letters that are grouped at that position in the pattern.

Although the patterns have fixed lengths, LAST's initial matches do not. LAST finds shorter matches by using a prefix of the pattern, and longer matches by cyclically repeating the pattern.

A restricted symbol omits letters of the main sequence alphabet, which are then forbidden at those positions:

    r  AG

An exact symbol groups no letters:

    Y  C T

In 2nd and subsequent cycles, restricted symbols are made unrestricted: if it is exact then the omitted letters are added as separate groups, else they are added as one group.

## BISF

This seeding scheme is for aligning bisulfite-converted DNA forward strands to a closely-related genome (MC Frith, R Mori, K Asai, NAR 2012 40:e100). It uses this seed alphabet:

    1  CT A G
    0  ACGT

And this pattern:

    1111110101100

It sets this lastdb default: -w2

It sets this lastal default: -pBISF

## BISR

This seeding scheme is for aligning bisulfite-converted DNA reverse strands to a closely-related genome (MC Frith, R Mori, K Asai, NAR 2012 40:e100). It uses this seed alphabet:

    1  AG C T
    0  ACGT

And this pattern:

    1111110101100

It sets this lastdb default: -w2

It sets this lastal default: -pBISR

## MAM4

This DNA seeding scheme is like MAM8, but a bit less sensitive, and uses about half as much memory. [From Frith & Noé 2014 NAR 42:e59 Table S11, row 12.] It uses this seed alphabet:

    1  A C G T
    0  ACGT
    T  AG CT

And these patterns:

    11100TT01T00T10TTTT
    TTTT110TT0T001T0T1T1
    11TT010T01TT0001T
    11TT10T1T101TT

## MAM8

This DNA seeding scheme finds weak similarities with high sensitivity, but low speed and high memory usage (e.g. ~50 GB for mammal genomes). [From Frith & Noé 2014 NAR 42:e59 Table S12, row 15.] It uses this seed alphabet:

    1  A C G T
    0  ACGT
    T  AG CT

And these patterns:

    1101T1T0T1T00TT1TT
    1TTTTT010TT0TT01011TTT
    1TTTT10010T011T0TTTT1
    111T011T0T01T100
    1T10T100TT01000TT01TT11
    111T101TT000T0T10T00T1T
    111100T011TTT00T0TT01T
    1T1T10T1101101

## MURPHY10

This protein seeding scheme is popular for finding long-and-weak similarities (LR Murphy et al. Protein Eng. 2000 13:149). It uses this seed alphabet:

    1  ILMV FWY A C G H P KR ST DENQ

And this pattern:

    1

It sets this lastdb default: -p

## NEAR

This DNA seeding scheme is good for finding short-and-strong (near-identical) similarities. It is also good for similarities with many gaps (insertions and deletions), because it can find the short matches between the gaps. (Long-and-weak seeding schemes allow for mismatches but not gaps.) It uses this seed alphabet:

    1  A C G T
    0  ACGT

And this pattern:

    1111110

It sets this lastal default: -r6 -q18 -a21 -b9

## YASS

This DNA seeding scheme is good for finding long-and-weak similarities. It is a good compromise for both protein-coding and non protein-coding DNA (L Noé & G Kucherov, NAR 2005 33:W540-W543). It uses this seed alphabet:

    1  A C G T
    0  ACGT
    T  AG CT

And this pattern:

    1T1001100101

## RY4-6 (abbreviation: RY4)

This DNA seeding scheme reduces run time and memory use, by only seeking seeds at ~1/4 of positions in each sequence [from Table 3 of MC Frith, L Noé, G Kucherov]. It uses this seed alphabet:

    R  A G
    Y  C T

And these patterns:

    RRRRRY
    RRYRRY
    RRYRYY
    RYRRRR
    RYRRRY
    RYRYRY
    RYYRRR
    RYYRRY
    RYYRYR
    RYYRYY
    RYYYRY
    RYYYYY
    YRYRRY
    YYYRRR
    YYYRRY
    YYYYRY

It sets this lastal default: -r6 -q18 -a21 -b9

## RY8-8 (abbreviation: RY8)

This DNA seeding scheme reduces run time and memory use, by only seeking seeds at ~1/8 of positions in each sequence. It uses this seed alphabet:

    R  A G
    Y  C T

And these patterns:

    RRRRRRRY
    RRYRRRYY
    RYRRRRYR
    RYRRRRYY
    RYRRRYRY
    YRRRRRRY
    YRRRRRYR
    YRRRRRYY
    YRRRYRRY
    YRRYRRYR
    YRRYRRYY
    YRYRRRYY
    YRYRRYRY
    YRYRRYYR
    YRYRRYYY
    YRYRYRYY
    YYRRRRYR
    YYRRRRYY
    YYRRRYRY
    YYRRRYYR
    YYRRRYYY
    YYRRYRYR
    YYRRYRYY
    YYRRYYRY
    YYRRYYYR
    YYRRYYYY
    YYRYRYYR
    YYRYRYYY
    YYRYYRYY
    YYYRYYYR
    YYYRYYYY
    YYYYYYYR

It sets this lastal default: -r6 -q18 -a21 -b9

## RY16-8 (abbreviation: RY16)

This DNA seeding scheme reduces run time and memory use, by only seeking seeds at ~1/16 of positions in each sequence. It uses this seed alphabet:

    R  A G
    Y  C T

And these patterns:

    RRRRRYRY
    RRRRYYRY
    RRRYYYRY
    RRRYYYYY
    RRYRRYRY
    RRYYYYRY
    YRRRRYRY
    YRRRYRYR
    YRRRYRYY
    YRRRYYRY
    YRRYYRYR
    YRRYYRYY
    YRRYYYRY
    YRRYYYYY
    YYRRYRYR
    YYRRYRYY

It sets this lastal default: -r6 -q18 -a21 -b9

## RY32-10 (abbreviation: RY32)

This DNA seeding scheme reduces run time and memory use, by only seeking seeds at ~1/32 of positions in each sequence. It uses this seed alphabet:

    R  A G
    Y  C T

And these patterns:

    YRRYRRYRRR
    YRRYRYYRRR
    YRRYYRYRRR
    YRRYYYRRRR
    YRRYYYRRRY
    YRRYYYYRRR
    YRYRRYRRRR
    YRYRRYRRRY
    YRYRRYYRRR
    YRYRYRYRRR
    YRYRYYRRRR
    YRYRYYRRRY
    YRYRYYYRRR
    YRYYRRYRRR
    YRYYRYYRRR
    YRYYYRYRRR
    YRYYYYRRRR
    YRYYYYRRRY
    YRYYYYYRRR
    YYRRYRYRRR
    YYRRYYRRRR
    YYRRYYRRRY
    YYRYRYRRRR
    YYRYYRYRRR
    YYRYYYRRRR
    YYRYYYRRRY
    YYYRYYRRRR
    YYYRYYRRRY
    YYYYRRYRRR
    YYYYYRYRRR
    YYYYYYRRRR
    YYYYYYRRRY

It sets this lastal default: -r6 -q18 -a21 -b9