Compare two bacterial sequence

Question

[saifulislam99121]

Hello, I am working with Acinetobacter baumannii. i want to compare this sequence with other Acinetobacter baumannii sequences. I need to know the differences between them . like which genes are missing which are not. I have fasta files and aligned file. I need to know how to visualize them.

Thank you.

[antonioggsousa]

Hi,

To visualize the similarity between two sequences you might want to do a dotplot, although this does not give you exactly the genes missing. For that you might want to try IGV. I used IGV in the past to visualize alignments of different samples against the same reference fasta sequence. The goal was different than yours. But it might be possible to find visually which are the genes missing with it.

I also found this tool, but I never used it myself (though it seems to provide functionality for what you want): https://genomevolution.org/coge/

I hope this helps,

António

[saifulislam99121]

Thank you for your suggestion Antonio. I have tried using IGV. But do not know why is is showing error? the error is "aligned_sorted.bam does not contain any sequence names which match the current genome". Can you help me regarding this??

I am trying to use coge now. Lets see what happens with this software.

Thank you.

Saiful

[antonioggsousa]

I guess that your alignment is not suitable for the program, or at least not using the options that you're trying now. Without seeing the files is difficult to tell more. I guess you performed a multiple sequence alignment of sequences and that is your alignment. What I did in the past was aligning fastq reads against a reference genome. Then, the bam aligned file comprised alignments against the reference and, therefore, sequences names matched the reference. This might not be your case. Perhaps the software provides other options to overcome this issue.

António

[saifulislam99121]

Thank you Antonio.

[Asaf]

You can try https://github.com/paulstothard/cgview_comparison_tool

[saifulislam99121]

Cloning into 'cgview_comparison_tool'... [e-mail]: Permission denied (publickey). fatal: Could not read from remote repository.

Please make sure you have the correct access rights and the repository exists.

I am getting this error while downloading. Do you have any suggestions?

[GenoMax]

I have fasta files and aligned file

You need to be more specific. Do you have fasta files for all genomes or just one? Is original data in fastq format and is aligned to that one reference?

You can take a look at mauve (LINK). Even though the link says software is not maintained, it should work for your purpose if you have fasta files for the genomes.

[saifulislam99121]

I have both fastq raw reads and fasta assemble reads. I have aligned the reference genome with the fastq file. Should I do otherwise? reference sequence is in fastq format. Thank you for your time.