{"id":59,"date":"2025-06-13T12:14:11","date_gmt":"2025-06-13T09:14:11","guid":{"rendered":"https:\/\/sisu.ut.ee\/bioinfo\/?page_id=59"},"modified":"2025-06-19T15:25:38","modified_gmt":"2025-06-19T12:25:38","slug":"tools-and-datasets","status":"publish","type":"page","link":"https:\/\/sisu.ut.ee\/bioinfo\/tools-and-datasets\/","title":{"rendered":"Applications"},"content":{"rendered":"

WEB-BASED APPLICATIONS<\/strong>
Primer3 version 4.1.0<\/a>
<\/strong>Primer3 is the most popular software for PCR primer design.<\/p>\n\n\n\n

Primer3 version 0.4
<\/strong>Older version of Primer3.<\/p>\n\n\n\n

PhenotypeSeeker
<\/strong>Predicts antimicrobial resistance and other phenotypes of bacterial isolates, using WMS or WGS data.<\/p>\n\n\n\n

StrainSeeker 1.1
<\/strong>Identification of bacterial species and strains from Illumina sequencing (WGS or WMS) data.<\/p>\n\n\n\n

SNPmasker 1.1<\/strong>
Masks known SNPS and other genomic regions that should be avoided when designing PCR primers<\/p>\n\n\n\n

GenomeTester 1.3<\/a><\/strong>
Fast e-PCR program for detecting binding sites of primers and potential PCR products<\/p>\n\n\n\n

MultiPLX 2.1<\/a><\/strong>
Software for grouping existing PCR primers into multiplex groups<\/p>\n\n\n\n

OligoTM 1.0<\/a><\/strong>
Predicts Tm of short oligonucleotides<\/p>\n\n\n\n

cRegions<\/strong>

PhyloCube<\/strong>

Y-mer<\/strong>
Predicts human chrY haplogroups, using a novel algorithm<\/p>\n\n\n\n



SOFTWARE and DATASETS FOR DOWNLOAD<\/strong>

KATK package version 4.2<\/strong>
KATK is a toolkit for discovering\u00a0and calling SNV and indel genotypes from human personal genomes. Unlike FastGT, KATK can detect\u00a0all<\/strong>\u00a0variants, even rare and de novo variants. It can process a deep-sequenced human genome in 1-3 hours.<\/p>\n\n\n\n