Provided by: obitools_1.2.12+dfsg-2_amd64 
NAME
ecoPrimers - description of ecoPrimers
Authors: Eric Coissac <eric.coissac@metabarcoding.org> and Tiayyba Riaz <‐
tiayyba.riaz@metabarcoding.org>
ecoPrimers designs the most efficient barcode markers and primers, based on a set of
reference sequence records, and according to specified parameters.
REFERENCE
Riaz T, Shehzad W, Viari A, Pompanon F, Taberlet P, Coissac E (2011) ecoPrimers:
inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids
Research, 39, e145.
ECOPRIMERS SPECIFIC OPTIONS
-d <filename>
Filename containing the reference sequence records used for designing the
barcode markers and primers (see obiconvert for a description of the database
format).
WARNING:
This option is compulsory.
-e <INTEGER>
Maximum number of errors (mismatches) allowed per primer (default: 0).
-l <INTEGER>
Minimum length of the barcode, excluding primers.
-L <INTEGER>
Maximum length of the barcode, excluding primers.
-r <TAXID>
Defines the example sequence records (example dataset). Only the sequences of
the corresponding taxonomic group identified by its TAXID are taken into account
for designing the barcodes and the primers. The TAXID is an integer that can be
found either in the NCBI taxonomic database, or using the ecofind program.
-i <TAXID>
Defines the counterexample sequence records (counterexample dataset). The
barcodes and primers will be selected in order to avoid the counterexample
taxonomic group identified by its TAXID.
-E <TAXID>
Defines an counterexample taxonomic group (identified by its TAXID) within the
example dataset.
-c Considers that the sequences of the database are circular (e.g. mitochondrial or
chloroplast DNA).
-3 <INTEGER>
Defines the number of nucleotides on the 3’ end of the primers that must have a
strict match with their target sequences.
-q <FLOAT>
Defines the strict matching quorum, i.e. the proportion of the sequence records
in which a strict match between the primers and their targets occurs (default:
0.7)
-s <FLOAT>
Defines the sensitivity quorum, i.e. the proportion of the example sequence
records that must fulfill the specified parameters for designing the barcodes
and the primers.
-x <FLOAT>
Defines the false positive quorum, i.e. the maximum proportion of the
counterexample sequence records that fulfill the specified parameters for
designing the barcodes and the primers.
-t <TAXONOMIC_LEVEL>
Defines the taxonomic level that is considered for evaluating the barcodes and
primers in the output of ecoPrimers. The default taxonomic level is the species
level. When using a taxonomic database builts from a NCBI taxonomy dump files,
the other possible taxonomic levels are genus, family, order, class, phylum,
kingdom, and superkingdom.
-D Sets the double strand mode.
-S Sets the single strand mode.
-O <INTEGER>
Sets the primer length (default: 18).
-m <1|2>
Defines the method used for estimating the Tm (melting temperature) between the
primers and their corresponding target sequences (default: 1).
1 SantaLucia method (SantaLucia J (1998) A unified view of polymer,
dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. PNAS, 95,
1460-1465).
2 Owczarzy method (Owczarzy R, Vallone PM, Gallo FJ et al. (1997) Predicting
sequence-dependent melting stability of short duplex DNA oligomers.
Biopolymers, 44, 217-239).
-a <FLOAT>
Salt concentration used for estimating the Tm (default: 0.05).
-U No multi match of a primer on the same sequence record.
-R <TEXT>
Defines the reference sequence by indicating its identifier in the database.
-A Prints the list of all identifiers of sequence records in the database.
-f Remove data mining step during strict primer identification.
-v Stores statistic file about memory usage during strict primer identification.
-h Print help.
OUTPUT FILE
The output file contains several columns, with ‘|’ as separator, and describes the
characteristics of each barcode and its associated primers.
column 1: serial number
column 2: sequence of primer 1
column 3: sequence of primer 2
column 4: Tm (melting temperature) of primer 1, without mismatch
column 5: lowest Tm of primer 1 against example sequence records
column 6: Tm of primer 2, without mismatch
column 7: lowest Tm of primer 2 against example sequence records
column 8: number of C or G in primer 1
column 9: number of C or G in primer 2
column 10: GG (Good-Good) means that both primer are specific to the example dataset,
GB or BG (Good-Bad or Bad-Good) means that only one of the two primers is
specific to the example dataset
column 11: number of sequence records of the example dataset that are properly
amplified according to the specified parameters
column 12: proportion of sequence records of the example dataset that are properly
amplified according to the specified parameters
column 13: yule-like output
column 14: number of taxa of the example dataset that are properly amplified according
to the specified parameters
column 15: number of taxa of the counterexample dataset that are properly amplified
according to the specified parameters
column 16: proportion of taxa of the example dataset that are properly amplified
according to the specified parameters (Bc index)
column 17: number of taxa of the example dataset that are properly identified
column 18: proportion of taxa of the example dataset that are properly identified (Bs
index)
column 19: minimum length of the barcode in base pairs for the example sequence records
(excluding primers)
column 20: maximum length of the barcode in base pairs for the example sequence records
(excluding primers)
column 21: average length of the barcode in base pairs for the example sequence
records(excluding primers)
EXAMPLES
Example 1:
> ecoPrimers -d mydatabase -e 3 -l 50 \
-L 800 -r 2759 -3 2 > mybarcodes.ecoprimers
Launches a search for barcodes and corresponding primers on mydatabase (see
obiconvert for a description of the database format), with a maximum of three
mismatches for each primer. The minimum and maximum barcode lengths (excluding
primers) are 50 bp and 800 bp, respectively. The search is restricted to the
taxonomic group identified by its taxid (2759 corresponds to the Diatoma). The two
last Nucleotides on the 3’ end of the primers must have a perfect match with their
target sequences. The results are saved in the mybarcodes.ecoprimers file.
Example 2:
> ecoPrimers -d mydatabase -e 2 -l 30 -L 120 \
-r 7742 - i 2 -E 9604 -3 2 > mybarcodes.ecoprimers
Launches a search for barcodes and corresponding primers on mydatabase (see
obiconvert for a description of the database format), with a maximum of two
mismatches for each primer. The minimum and maximum barcode lengths (excluding
primers) are 30 bp and 120 bp, respectively. The search is restricted to the
Vertebrates, excluding Bacteria and Hominidae (7742, 2, and 9604 corresponds to the
TAXID of Vertebrates, Bacteria, and Hominidae, respectively. The two last
nucleotides on the 3’ end of the primers must have a perfect match with their
target sequences. The results are saved in the mybarcodes.ecoprimers file.
AUTHOR
The OBITools Development Team - LECA
COPYRIGHT
2019 - 2015, OBITool Development Team
1.02 12 Jan 28, 2019 ECOPRIMERS(1)