Tools for bacteria comparative genome

[mahathir]

*Hye all.
*I'm an undergraduate Bioinformatics student.
*Currently I'm doing my final year project with title of comparative genomic of MTB strains.
*I have the whole genome for the 3 strains that I'm going to compare.
* The works that I'm planning to do now is :
1) Gene annotation
2) Multiple genome alignment
3) Pairwise genome comparison
4) Identify the phage sequences
5) Identification of resistance gene sequence
6) Sequence typing
*The problem that I'm facing now is, I'm required to use different tools for each of the task above.
*I really hope someone from seqanswer can help me to guide me. I'm new to this forum, and I really want to learn more in Bioinformatics.
*Thank you in advance.

[GenoMax]

MAUVE for multiple genome comparison.

Since this is a project assignment and you have to use a different tool for each I will leave the task of searching this forum to you without giving you additional answers. You should be able to find independent tools for each of those tasks after spending some time searching. If you have trouble with direct searches on the forum then google is what you would want to use to search this forum.

[piet]

Currently I'm doing my final year project with title of comparative genomic of MTB strains.

Dear Mahathir,

in my opinion Mycobacterium tuberculosis is a bad choice for such a project, especially if focus is on learning different computational methods. By its biology, Mycobacterium tuberculosis is a rather special bacterium which differs from "normal" bacteria in many respects. If you can, you should choose another species for your project. If you have to stick to Mycobacterium tuberculosis, you have to adopt your methods to the peculiarities of this bacterium. The genomes are extremely conserved and show very little mutations. All known isolates of Mycobacterium tuberculosis belong to a single clonal complex, their genomes are nearly identical and they differ mostly by SNP.

I have the whole genome for the 3 strains that I'm going to compare.

you should read the paper published along with the release of the first complete genome of M.tuberculosis. This paper will give you several hints about comparison of genomes. The paper is linked to the Genbank entry, see http://www.ncbi.nlm.nih.gov/nuccore/AL123456.3

1) Gene annotation
2) Multiple genome alignment
3) Pairwise genome comparison
4) Identify the phage sequences
5) Identification of resistance gene sequence
6) Sequence typing

most of this is not really relevant for Mycobacterium tuberculosis. There are no phages; antibiotic resistence is caused solely by single-point mutations in several genes, there are no horizontally acquired genes; there does not exist a MLST scheme (multilocus sequence typing); a common typing method is based in the direct repeats of the CRISPR element;

To do meaningful analysis of Mycobacterium tuberculosis you have to learn about its biology. Any research into Mycobacterium tuberculosis needs patience and lots of endurance, even bioinformatics.

[mahathir]

Dear Mahathir,

in my opinion Mycobacterium tuberculosis is a bad choice for such a project, especially if focus is on learning different computational methods. By its biology, Mycobacterium tuberculosis is a rather special bacterium which differs from "normal" bacteria in many respects. If you can, you should choose another species for your project. If you have to stick to Mycobacterium tuberculosis, you have to adopt your methods to the peculiarities of this bacterium. The genomes are extremely conserved and show very little mutations. All known isolates of Mycobacterium tuberculosis belong to a single clonal complex, their genomes are nearly identical and they differ mostly by SNP.


you should read the paper published along with the release of the first complete genome of M.tuberculosis. This paper will give you several hints about comparison of genomes. The paper is linked to the Genbank entry, see http://www.ncbi.nlm.nih.gov/nuccore/AL123456.3


most of this is not really relevant for Mycobacterium tuberculosis. There are no phages; antibiotic resistence is caused solely by single-point mutations in several genes, there are no horizontally acquired genes; there does not exist a MLST scheme (multilocus sequence typing); a common typing method is based in the direct repeats of the CRISPR element;

To do meaningful analysis of Mycobacterium tuberculosis you have to learn about its biology. Any research into Mycobacterium tuberculosis needs patience and lots of endurance, even bioinformatics.

Thank you for your kind reply. I have to stick to Mycobacterium tuberculosis strains sir for this project. Is there suggestion u can give me for the comparative genome for 3 strains of MTB. I took one drug susceptible strain and 2 multidrug resistant strains to be compared

[piet]

Is there suggestion u can give me for the comparative genome for 3 strains of MTB. I took one drug susceptible strain and 2 multidrug resistant strains to be compared

The TB Dream website may be a good starting point to learn more about mutations causing AB resistance in MTB.

https://tbdreamdb.ki.se/Info/

[mahathir]

The TB Dream website may be a good starting point to learn more about mutations causing AB resistance in MTB.

https://tbdreamdb.ki.se/Info/

Thank you again sir.
By the way, since I have to do my project with this 3 strains, what are the comparative works that I can do with the strains.