Is the input file required to be a CDS file？

[fujch7]

No description provided.

[donovan-h-parks]

FASTA file with genes as amino acids.

[fujch7]

Dear Donovan Parks， Thanks for your reply. According to the user guide, the input file is required to be genomic nucleotide sequence. My question is whether the nucleotide sequence should contain non coding genes, such as rDNA. There is a little difference between the two results. Best regards Jiacheng

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------------------&nbsp;Original&nbsp;------------------ From: &nbsp;"Donovan Parks"<[email protected]&gt;; Date: &nbsp;Mon, Apr 27, 2020 10:23 PM To: &nbsp;"dparks1134/CompareM"<[email protected]&gt;; Cc: &nbsp;"fujch7"<[email protected]&gt;; "Author"<[email protected]&gt;; Subject: &nbsp;Re: [dparks1134/CompareM] Is the input file required to be a CDS file？ (#29) &nbsp; FASTA file with genes as amino acids. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[donovan-h-parks]

Hi. Sorry, there are different ways to run CompareM. You can provide genome assembles as nucleotide sequences and CompareM will call genes using Prodigal. Alternatively, you can provide your own called genes in which case they should be provided as amino acid sequences. Ultimately, the AAI is calculated between called genes represented as amino acids. There is no need to explicitly remove non-coding genes. Note, that CompareM does NOT accept called genes as nucleotide sequences. CompareM may run on such sequences, but this is not valid input.

[swmuyu]

FASTA file with genes as amino acids.

I try (comparem aai_wf Ca_CQIV_MF197913.fasta out), but fail
Could you please send me a sample of input file to my e-mail ([email protected])? i need it very much.

[fujch7]

FASTA file with genes as amino acids.

I try (comparem aai_wf Ca_CQIV_MF197913.fasta out), but fail
Could you please send me a sample of input file to my e-mail ([email protected])? i need it very much.

只输入了一条序列吗，我是把多条序列放一个文件夹里的。

[swmuyu]

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