Suggestion for a good genomics program?

[pseizure]

I need a simple program where I can paste the genome of an organism and translate it into an amino acid sequence. Taking out introns and exons would be helpful I think?

Someone mentioned a program to me in person that sounded like exsisy? but I haven't found anything.

[deleted-140482]

My guess is they were recommending ExPASy. Go to ExPASy.org For what you want, you can pick the "Translate" tool out of the list and use that. There may be other useful tools on the webpage too for what you want, but I've used translate in the past. You will have to do some cleaning up and probably finding the right open reading frame.

[pseizure]

I think you are right. However all I have is a 500mb fasta file of the entire genome of an organism that is not on ncbi. I don't think ExPaSy can handle that translation.

I think I know roughly where my gene of interest is on a homologous organism, but it's difficult to figure out where 51849854..51853553 is on a 500mb text file. I think I might need an actual software program?

[SciB]

Hi,

You have the entire genome sequence of an organism, but am I correct in assuming that you are only interested in one or a couple of proteins? You do not mean that you want to translate the entire genome into amino acid sequences, do you? That would be a horrendous and pointless exercise I would think. What is your goal? If you know what proteins you are looking for then you can do a search and find their DNA sequence then BLAST your genome sequence and find where they are.

Once you locate the open-reading frames (http://bioweb.uwlax.edu/genweb/molecula ... ation.html)
you can do the translation and get the corresponding amino acid sequences.

Is this what you are aiming at or am I misunderstanding what you are trying to do?
Sybee

[pseizure]

Hi,

You have the entire genome sequence of an organism, but am I correct in assuming that you are only interested in one or a couple of proteins? You do not mean that you want to translate the entire genome into amino acid sequences, do you? That would be a horrendous and pointless exercise I would think. What is your goal? If you know what proteins you are looking for then you can do a search and find their DNA sequence then BLAST your genome sequence and find where they are.

Once you locate the open-reading frames (http://bioweb.uwlax.edu/genweb/molecula ... ation.html)
you can do the translation and get the corresponding amino acid sequences.

Is this what you are aiming at or am I misunderstanding what you are trying to do?
Sybee

Actually I am dealing with a genome that has not been mapped yet, since it was just sequenced last year. Haha so it's basically a 500 mb text file of nucleotides. The gene I am looking for is known in other organisms that are closely related but of course it's a little different. I am assuming it's in a similar area on the chromosome of my organism of interest on chromosome 1 around 50 mil. I do think translating this huge file to amino acids would make it less taxing on my computer at least, and maybe searchable, but a program that was meant for this sort of thing would go a long way.

[SciB]

If you know what protein you are looking for why don't you just take some 50 base pair ssequences from several places in the gene and do a BLAST on your genomic DNA? You You don't need to translate the whole genome, or am I still misunderstanding you? Yes, the known genes are are somewhat different from the gene in your new genome but there is probably some homologous regions . How else can you find an unknown sequence?

[SciB]

If you know what protein you are looking for why don't you just take some 50 base pair ssequences from several places in the gene and do a BLAST on your genomic DNA? You You don't need to translate the whole genome, or am I still misunderstanding you? Yes, the known genes are are somewhat different from the gene in your new genome but there is probably some homologous regions . How else can you find an unknown sequence?

[pseizure]

If you know what protein you are looking for why don't you just take some 50 base pair ssequences from several places in the gene and do a BLAST on your genomic DNA? You You don't need to translate the whole genome, or am I still misunderstanding you? Yes, the known genes are are somewhat different from the gene in your new genome but there is probably some homologous regions . How else can you find an unknown sequence?

I would like to but from what I've seen, the BLAST database doesn't have my organism's genomic DNA. I guess I could try finding a really good computer with an SSD drive so I could run really fast ctrl+f searches, not sure how fast it would actually be though.

[deleted-140482]

I'm not 100% sure I'm following exactly what you are trying to do, but you know that you don't have to BLAST against a known organism's genome. You can also BLAST to "align two or more sequences." Then, if I'm understanding correctly, you could put the genome sequence you have (or possibly portions of it) as the subject sequence and then the homologous gene you are interested in as the query sequence. You'll probably want to select an option other than "highly similar sequences" in what you optimize for, but you could easily run it multiple ways.

Again, sorry if I misunderstood what you are looking for.

http://blast.ncbi.nlm.nih.gov/Blast.cgi ... =blastHelp

[pseizure]

I'm not 100% sure I'm following exactly what you are trying to do, but you know that you don't have to BLAST against a known organism's genome. You can also BLAST to "align two or more sequences." Then, if I'm understanding correctly, you could put the genome sequence you have (or possibly portions of it) as the subject sequence and then the homologous gene you are interested in as the query sequence. You'll probably want to select an option other than "highly similar sequences" in what you optimize for, but you could easily run it multiple ways.

Again, sorry if I misunderstood what you are looking for.

http://blast.ncbi.nlm.nih.gov/Blast.cgi ... =blastHelp

Thanks this was helpful. Although it seems uploading a 500mb file to search within is not exactly something the website can handle. I could try splitting it up, although that could be very tedious.

Stuck again haha :\