DECIPHER maximum allowable size

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curiousmind007 ▴ 10

@d27aed9d

Last seen 2.4 years ago

Germany

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!

DECIPHER Alignment alig • 1.9k views

ADD COMMENT • link updated 3.6 years ago by Erik Wright ▴ 150 • written 3.6 years ago by curiousmind007 ▴ 10

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This error typically occurs when aligning genomes that are not collinear. How long are the sequences you are aligning?

ADD REPLY • link 3.6 years ago Erik Wright ▴ 150

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Approximately 104073951 bp. I want to compare several genes. Is DECIPHER limited to short sequences?

ADD REPLY • link 3.6 years ago curiousmind007 ▴ 10

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AlignSeqs() can handle longish sequences if they are collinear. If not, you can use FindSynteny() followed by AlignSynteny().

ADD REPLY • link 3.6 years ago Erik Wright ▴ 150

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I run FindSynteny() and I got following Error:

'dbFile' must be a character string or SQLiteConnection.

I used a Large DNAStringSet as input for the FindSynteny()

ADD REPLY • link 3.6 years ago curiousmind007 ▴ 10

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FindSynteny() takes a database as input rather than a DNAStringSet. I recommend reading the documentation for alignment.

ADD REPLY • link 3.6 years ago Erik Wright ▴ 150

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