Hi, I have run Vmatch and Usearch on the same NGS dataset (Illumina 101 bp PE) against a local database of protein sequences and noticed that there is a significant difference in numbers of hits they generate.

I used the following commands:

VMATCH

vmatch -showdesc 0 -dnavsprot 11 -l 20 -identity 90 -h 2 -q input.fasta dbs/database > vmatch.out

Then I took only the best match. Database was made up using mkvtree in Vmatch.

USEARCH

usearch -usearch_global input.fasta -db db.udb -id 0.90 -threads 16 -blast6out usearch.out -maxaccepts 1

In Vmatch I allowed only 2 mismatches as you can see, whereas in USEARCH I allowed to get hits down to 90% identity, still why there is a huge difference in results?

OUTPUTS (Column means: GENE name [TAB] Normalised counts [TAB] RAW hit counts): all hits

VMATCH OUTPUT

ISCR1   7.99383167412687        4054
ISCR14  1.74291497975711        861
ISCR2   50.7803527891896        23294
ISCR3   0.0991902834008098      49
ISCR4   2.81212121212114        1392
ISCR5   0.222003929273085       113
ISCR6   2.48478701825562        1225
ISCR7   0.0078740157480315      3
ISCR8   0.0854368932038835      44
OXA-10  0.00778210116731518     2
SHV     0.00699300699300699     2
aac(3)-IVa      0.00387596899224806     1
aph(3')-Ia      0.0260012252632179      7
catB2/catB3/catB10      0.109523809523809       23
catB9   0.0909090909090909      19
dfrA1/dfrA15    0.203821656050955       32
dfrA12/dfrA13/dfrA21/dfrA22/dfrA33      0.00606060606060606     1
dfrA16  0.00636942675159236     1
dfrA3   0.296296296296297       48
dfrA6/dfrA31    0.00636942675159236     1
dfrC    0.00628930817610063     1
intI1   0.00891090857708068     3
intI10  1.41562500000001        453
intI2   0.624615384615386       203
intI3   0.401734104046244       139
intI6   0.137704918032787       42
intI7   0.161716171617162       49
intI8   0.0379746835443038      12
intI9   0.912757686598001       330
sul2    0.00738007380073801     2
tet(36) 0.0015625       1
tet(39) 0.00253164556962025     1
tet(C)  0.0277777777777778      11
tet(M)  0.00312989045383412     2
tetB(P) 0.380368098159508       248
vanRN   0.00434782608695652     1
vat(C)  0.00471698113207547     1
vat(F)  0.298642533936652       66
vat(G)  0.0833333333333333      18

USEARCH Output

ISCR1   1.24366471734895        638
ISCR2   30.2932796346512        15002
ISCR3   0.0587044534412955      29
ISCR4   0.0565656565656565      28
ISCR6   0.00202839756592292     1
ISCR7   0.0026246719160105      1
ISCR8   0.0737864077669903      38
aph(3')-Ia      0.029520295202952       8
dfrA1/dfrA15    0.152866242038217       24
dfrA3   0.0123456790123457      2
dfrA6/dfrA31    0.00636942675159236     1
intI1   0.00593471810089021     2
intI10  0.209375        67
intI2   0.116923076923077       38
intI3   0.0173410404624277      6
intI6   0.00327868852459016     1
intI8   0.00949367088607595     3
intI9   0.602232901241181       218
tet(39) 0.00253164556962025     1
tet(C)  0.0227272727272727      9
tet(M)  0.00312989045383412     2