AutoCloner: automatic homologue-specific primer design for full-gene cloning in polyploids

BMC Bioinformatics
Alexander Coulton, Keith J Edwards

Abstract

Polyploid organisms such as wheat complicate even the simplest of procedures in molecular biology. Whilst knowledge of genomic sequences in crops is increasing rapidly, the scientific community is still a long way from producing a full pan-genome for every species. Polymerase chain reaction and Sanger sequencing therefore remain widely used as methods for characterizing gene sequences in many varieties of crops. High sequence similarity between genomes in polyploids means that if primers are not homeologue-specific via the incorporation of a SNP at the 3' tail, sequences other than the target sequence will also be amplified. Current consensus for gene cloning in wheat is to manually perform many steps in a long bioinformatics pipeline. Here we present AutoCloner ( www.autocloner.com ), a fully automated pipeline for crop gene cloning that includes a free-to-use web interface for users. AutoCloner takes a sequence of interest from the user and performs a basic local alignment search tool (BLAST) search against the genome assembly for their particular polyploid crop. Homologous sequences are then compiled with the input sequence into a multiple sequence alignment which is mined for single-nucleotide polymorphisms (SNPs). Various ...Continue Reading

References

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Aug 18, 2018·Science·UNKNOWN International Wheat Genome Sequencing Consortium (IWGSC)Cristobal Uauy

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Methods Mentioned

BETA
PCR

Software Mentioned

R
Fasta
primer3
dplyr
tibble
Muscle
Dialign
optparse
AutoCloner
PolyMarker

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