Hey,
Let's say I have one gene, TP53 for example.
What I want to do is-
1.Find the gene's orthologs.
2. Align them all.
I downloaded the orthologs from ENSEMBL, they are stores in a single dictionary.
I saw that MSA can be performed using Clustal Omega, however, I am not sure how to get my input data to be in one of the right formats.
So my questions are:
1. What is the most convenient way to get my data in an acceptable format (like fasta), without doing it manually and getting all the orthologs at once?
2. Generally, is there a better way to do want I want to do? Practically, I will need to perform 1,400,000 alignments (~300 sequences each time).
Thank you very much!
Hmmer tool is well suited for your query to align the sequences. following links can be used for your guidance-
http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf
Article Johnson LS, Eddy SR, Portugaly E.. Hidden Markov model speed...
1. What is the most convenient way to get my data in an acceptable format (like fasta), without doing it manually and getting all the orthologs at once?
- For downloading any data, it depends what and from where you want to get the data and how proficient you are in accessing the available channels. There is a ftp site from which you can get the data in several formats.
- But if you already have downloaded the data, what format is it?
- Which computer system are you using?
- You can simply paste all of your sequences in single file. This file can be used for MSA in any program like clustal, mafft, muscle etc.
2. Generally, is there a better way to do want I want to do? Practically, I will need to perform 1,400,000 alignments (~300 sequences each time).
- I don't understand what are you actually trying to do, and guess you are doing or thinking something wrong.
- What is your aim?
Firstly you have to use linux for all these steps.
You have downloaded genes from ENSEMBL not orthologs. You have to find orthologs that are related to p53 with a limited cutoff, cutoff which varies according to the occurence of the gene.
You can find orthologs of the fastas/genes using orthomcl , get_homologues.
Then the best hit genes can be use further for alignment.
You need to concatenate all the genes in a single fasta using $ cat *.fasta > output.fasta (for fasta format and can be change accordingly) , before that name the identifiers properly you can find the scripts online for modification of identifiers or you can use libreoffice for that.
Then you can run standalone versions of any muscle mafft clustalw for alignment.
And you can see the relatedness of your gene with other genes using iqtree, itol, mega etc
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