Tools For Interspecies Genomic Alignment

Question

[Pcrer]

Hi, guys,

I am looking for a nice tool(s) for multiple genomic alignment.

The only requirement is that I do not need to copy the sequences, just simply type the gene ID or a specific chromosome region and i could get a inter-species genomic alignment for check the conversion.

Many thanks.

[Paulo Nuin]

Do you want to align short (1-2kb max) or very large sequences (Mb)?

[Darked89]

re retagging: Looks like there is a length limit for combined tags. "genomic-alignment-multiple" is being truncated.

[Pcrer]

sometimes even a huge sequences up to 1Mb.

Answer 1

[Darked89]

Looks like you want to find already precomputed alignments for a given region. In that case you are limited to web sites which serve such content. In ENSEMBL (I already picked a human gene SYNGR2):

http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000108639;r=17:76164671-76169009;t=ENST00000225777

• Left top box: "Comparative Genomics -> Genomic alignments (51)" click on the last one
• on a new page select drop down menu "Select an alignment" and pick i.e. "16 amnionta vertebrates Pecan".
• You may go to "Go to a graphical view (Genomic align slice) of this alignment" to have an overview what is going on in this region (there are many unsequenced gaps in various genomes).
• In case you decide to use the sequence after all, "Export data" (left, top) in a format you find usable.

There are Ensembl sites also for plants, fungi and bacteria, but these are less developed as the main vertebrate oriented main site.

Answer 2

[Mary]

I think VISTA can do this for you. http://genome.lbl.gov/vista/index.shtml

There are various ways you could use the different VISTA tools/interfaces depending on your species. But one of them should work.

VISTA sponsors a free tutorial if you want to get an overview of what it can do: http://www.openhelix.com/vista

Answer 3

[Pierre Lindenbaum]

There are numerous tools to download a sequence from an ID. E.g: NCBI EFETCH, DAS-DNA ... you could then send those sequences to a Mutliple Sequence Aligner like Clustal

I guess that there are also some scripts for taverna doing this. e.g. http://www.myexperiment.org/workflows/203.html

Answer 4

[Daniel Standage]

Some popular multiple sequence alignment (MSA) tools are:

• ClustalW2
• Muscle
• T-coffee
• MAFFT
• KALIGN

Most of these tools do not download the sequences by ID for you. If you are not comfortable downloading the sequences yourself, you probably want to look at applications like:

• DNASP
• MEGA
• BioEdit

These are free desktop tools, but to be honest, I've never used them on genome-sized data sets. They may crash your computer! If you have some money to spend, you can check these out:

• Geneious
• CLC Genomics Workbench

[Pcrer]

Thanks a lot. u mean huge online sequences alignment may damn the PC?

[Daniel Standage]

More or less. I don't know what kind of overhead those free GUI applications (DNASP, MEGA, BioEdit) have, so I don't if they will crash the PC when you give them genome-sized data. Stuff like Geneious and CLC is designed to work with genome-sized data, but the other GUI apps were made back when most biologists used Excel spreadsheets to organize their DNA sequences.

My recommendation is to familiarize yourself with working from the command line. It takes a bit of initial investment, but the returns (in terms of the tools you can use) are well worth it.

Answer 5

[Casey Bergman]

Try Mobyle for relatively short sequences.

[Pcrer]

thanks for this.