multiple alignment of genomes via LASTZ

Question

[rj.rezwan]

Hi, I am using two different genomes of dragon fruit species and want to compare them by multiple alignment via "LASTZ" tool but the script giving error while using the following code. please help me to fix this code

lastz Guanhuabai.fa david_bowie.fa --notransition --multiple --ambiguous=iupac --step=20 --nogapped --format=maf > Guanhuabai_vs_david_bowie.maf

[Asaf]

What is the error message?

[rj.rezwan]

Genome files contain multiple fasta sequences in the form of different chromosome names, e.g., >chr01, >chr02, etc. So I put the --multiple command for this but after running the command I am getting the error as cannot understand ---multiple command. If I remove the multiple command then this tool suggests to use --multiple command because user using multiple fasta sequences in one file. So this is the main problem.

[Asaf]

From what I see multiple is a command, and should be given after the file name like this example from the documentation page: lastz critter.fa[multiple,unmask,nameparse=darkspace] /dev/stdin --masking=3

[rsharris]

In the parlance of the lastz documentation, "multiple" is an action.

[rsharris]

... this tool suggests to use --multiple command ...

Actually, it the suggestion lastz makes uses different terminology. What is actually suggested was "consider using the multiple action". The readme file contains a table of actions, and "multiple" is the second action in that table.

Answer 1

[manaswwm]

I remember using lastz a while ago for aligning genomes, but I never used this --multiple option. Instead, I split the genome file into separate files each containing a single chromosome (for both species) and then performed an 'all against all' chromosome-specific alignment and it worked fine for me

[rj.rezwan]

I have tried splitting the chromosomes into different files and it works without the --multiple option. Thank you.