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FastGT package version 4.0

FastGT is a toolkit for counting k-mers from FASTQ files and calling 30 millions human SNV genotypes. It can process 30x human genome in less than an hour.

Citation:


GenomeTester package version 4.0

GenomeTester4 is a toolkit for counting k-mers from nucleic acid sequences and performing basic set operations (union, intersection and difference) on k-mer lists. It can be used in many bioinformatic analyses.
GenomeTester4 is released under GNU General Public License version 3.

Citation: Kaplinski L, Lepamets M, Remm M. (2015). GenomeTester4: a toolkit for performing basic set operations – union, intersection and complement on k-mer lists. GigaScience; 4:58


GenomeTester package version 1.3

GenomeMasker (gmasker) masks over-represented words in the FASTA file, preventing design of primers in repeated regions. GenomeTester (gtester) is the program that tests 1) whether PCR primers have excessive number of binding sites on template sequence and 2) how many PCR products would be amplified from the template DNA and where are they located. Package contains also modified the PRIMER3 program (gm_primer3), to be able to design primers from lowercase-masked sequences.

Citation: Andreson R, Reppo E, Kaplinski L, Remm M. (2006). GENOMEMASKER package for designing unique genomic PCR primers. BMC Bioinformatics; 7:172.


StrainSeeker

StrainSeeker is a program for identification of bacterial strains from raw sequencing reads. StrainSeeker database contains custom-built phylogenetic tree of all bacterial strains and k-mers specific to each node of the tree.

Citation: Roosaare M, Vaher M, Kaplinski L, Möls M, Andreson R, Lepamets M, Koressaar T, Naaber P, Koljalg S, Remm M. (2016). StrainSeeker: fast identification of bacterial strains from unassembled sequencing reads using user-provided guide trees. http://biorxiv.org/content/early/2016/02/19/040261.


Primer3_masker
K-mer lists for masking genomic sequences with Primer3_masker will be available from the Primer3_masker webpage.


MultiPLX version 2.0

MultiPLX is a tool for analyzing PCR primer compatibility and automatically finding optimal multiplexing (grouping) solution. It uses state-of-the-art nearest neighbour DNA binding thermodynamics to estimate possible unwanted pairings between PCR samples.
Citation: Kaplinski L, Andreson R, Puurand T, Remm M. (2005). MultiPLX: automatic grouping and evaluation of PCR primers. Bioinformatics. 2005 Apr 15;21(8):1701-2.


SLICSel version 1.1

SLICSel is a program for designing specific oligonucleotide probes for microbial detection and identification. To obtain maximal specificity of designed oligonucleotides, SLICSel uses the Nearest-Neighbor thermodynamics-based approach for probe design.
Citation: Scheler O, Kaplinski L, Glynn B, Palta P, Parkel S, Toome K, Maher M, Barry T, Remm M, Kurg A. (2011). Detection of NASBA amplified bacterial tmRNA molecules on SLICSel designed microarray probes. BMC Biotechnology 2011;11:17.


FastaGrep version 2.0

FastaGrep is a tool for searching oligonucleotide binding sites from FastA genomic sequences. It can do both match/mismatch based and thermodynamic binding energy searches.