What are the best bioinformatics tools for aligning and comparing whole bacterial genome sequences and their annotations?

More Carol Ecale Zhou's questions See All

What does "CB" mean when referring to the product of a tRNA gene or gene homolog?

I have a file produced by a tRNA search/prediction code. The output includes results that identify a gene as something like, tRNASerTCT_CB or tRNA_CB. What does this mean?

07 August 2017 2,285 0 View

What software do you recommend for illustrating genes along a genome?

03 April 2016 7,941 8 View

Does anyone know of a database that links structure domains, sequences, known function, active sites, and function identifiers?

Specifically I am looking for linkage between data sets contained in databases like SCOP, BRENDA, CSA, EC, KEGG. I can manually search what I need in each, but that is labor intensive and not...

05 June 2013 9,869 1 View

IHC on mouse liver hepatocytes?

Can anyone help me choose primary antibodies for mouse liver hepatocytes and also in conjunction Cd8 cells. Also Cd3 cells. I want to look at hepatocytes and adjacent immune cells in mice with...

01 March 2021 6,953 1 View

What is the difference between genotype and haplotype data in the ped format?

Hi everybody In the ped format for genotype, alleles of any SNP are represented by two columns (one for each allele, separated by a space). Is a column sufficient for the haplotype to...

27 February 2021 1,965 1 View

Are there any databases for gene co-expression or expression pattern clustering?

I am currently working on gene clustering based on co-expression pattern in mouse brain. The problem is I do not have some solid way to test my result. Are there any suggestions for databases...

22 February 2021 4,374 3 View

How to obtain Contig sequence from BAM file?

I have use HISAT2 for alignment . Now i want to obtain contig sequence from from BAM file in galaxy server? I have used Samtools View. That is giving me some sequence but I am not sure whether it...

12 February 2021 3,262 4 View

Various schools have emerged in the study of comparative literature. Mention the most prominent of them in a nutshell.?

Various schools have emerged in the study of comparative literature. Mention the most prominent of them in a nutshell. And he talked about one of them?

09 February 2021 1,099 8 View

Plasmid amplification in S2 cell?

When co-transfect S2 cell with selection vector (pCoHygro or pCoBlast ) to make a stable cell line, does the gene integrate into the genome or just like E.coli? How do the plasmids amplify within...

09 February 2021 5,423 1 View

Useful architecture for bioinformatics?

Hi Dear researchers In ensemble-based architectural design Which algorithms are more useful for classification? What is the difference between parallel and ensemble architecture? Thanks I am...

08 February 2021 2,727 5 View

I am looking for a co-author specialised in decision-making/managerial studies/data science/?

I am currently working on a publication with the intention of presenting a proprietal method for a ranked comparison of incompatible features in a limited data set. I am looking for a co-author as...

08 February 2021 1,450 5 View

Electron density difference maps(Fo-Fc): what is the meaning of negative densities (red blobs)?

Dear community, As far as I understand, negative density features point at stuff that is in the model, but not supported by experimental data. However, in many cases (e.g. attached image), when...

06 February 2021 2,847 2 View

Consensus sequence from ClustalX?

I am doing multiple sequence alignment to design primer for my gene. Can anyone tell me how to select the consensus sequence after alignment. I am using ClustalX for the alignment.

04 February 2021 8,872 2 View

Ghulam Dhabaan

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

Carol Ecale Zhou

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.

Julian Gough

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!

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.

Areej Alsheikh-Hussain

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