Need help to perform a probeseq aligment

Question

[rodrigohb.93]

Hello! I am currently to perform an alignment for which i have thousands 60 nucleotide-long sequences from the probes of a microarray plataform (Agilent-045997 Arraystar human lncRNA microarray V3 (Probe Name Version), GEO GPL16956) and a fasta file with the nucleotide sequences of all transcripts on human reference genome from GENCODE (https://www.gencodegenes.org/human/). I would like to perform an alignment in R of the probe sequences of mRNAs to the transcript sequences so that i could know the transcript that the probe represents. I have never performed any alignment before and so i do not know any R packages that could help with this task. Does anyone know how i could perform this?

Thank you so much for your help and sorry for any english mistakes.

Answer 1

[GenoMax]

Since you are looking for very similar matches I suggest that you use blat from Jim Kent at UCSC. You will need to use it on plain unix command line.

If you don't want to use the command line then do the searches at UCSC web blat site. You may need to perform the searches in batches.