I have tried VISTA, progressiveMauve, and Geneious Pro, with varying success. Helpful error messages are a plus when trying to get any tool to work at first.
Hi Carol,
For full genomic comparative study, you may use Artemis, it can help you perfectly, you just need to know how to use it. other option is VISTA. Best
Artemis is a great viewer, but it takes an alignment as input. I need a code that computes the alignment and renders the result in SAM/BAM format for input to Artemis.
Mummer is a great suggestion, thank you, along with Artemis/ACT, and both were relatively easy to install and get running.
What do you mean by 'annotations'. If you mean proteins, their domains and functions, then you can find your bacterium in this list:
http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/gen_list.cgi#model_prokaryotes
click on it then try the two tabs at the top 'Unusual Superfamilies' and 'Domain Pairs' then follow links to compare it to any group of other bacteria by taxonomy. Also you can explore comparative enrichment of function, phenotype and other ontological terms including e.g. drugs.
If your bacterial genome is not listed, and it has gene models, then we'll add it for you. If you tell me the species and the comparisons you want to make then I can post links to examples for you.
Hi Julian, Eventually I'll be performing comparisons across genomes, gene profiles, and protein functions. I am comparing Bacillus anthracis Ames to other Ba isolates. Having Ba Ames in your list would be most helpful. Others I will look at and perform isolate comparisons include Acinetobacter baumanii, Burkholderia pseudomallei/mallei, and Yersinia pestis. So it would be great to have the reference genomes fully annotated at all levels, including protein, and your resource could really come in handy. Thanks for helping out!
As for bacterial genome. The best software is mauve， which could align multiple genomes.
Thank you Xiangyang. I will try Mauve. Artemis/ACT is working quite well for me, but aligning multiple genomes at the same time is also handy.
Yes,currently Mauve was the best choice for multiple genome comparison with genomic annotation
Anybody knows which tool will be the best one to do the genomic phylogenic tree? Thanks.
Hi Vincent,
Map sequences to a reference genome using SHRIMP. Identify SNPs using Nesoni (which produces a SNP alignment). Generate a tree from the SNPs data using RAxML.
Cheers.
Areej
Hi,
I want to build phylogeny whole genome of mammals anybody suggest which software best for alignment
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