Entering edit mode
Hi there I want to align up to 9 sequences using the package DECIPHER. I have managed to read the fasta files and apply readDNAStringSet
. When I then run AlignSeqs
I get following error
Aligning Sequences:
|====================== | 20%
Error in f(p.profile[, anchors[2, n - 1]:anchors[1, n], drop = FALSE], :
Alignment larger (3,062,288,908) than the maximum allowable size (2,147,483,647).
Can you help me understand where the issue is and how to solve this?
Thank you!
This error typically occurs when aligning genomes that are not collinear. How long are the sequences you are aligning?
Approximately 104073951 bp. I want to compare several genes. Is DECIPHER limited to short sequences?
AlignSeqs()
can handle longish sequences if they are collinear. If not, you can useFindSynteny()
followed byAlignSynteny()
.I run
FindSynteny()
and I got following Error:I used a Large DNAStringSet as input for the
FindSynteny()
FindSynteny()
takes a database as input rather than aDNAStringSet
. I recommend reading the documentation for alignment.