Explore a gene with its cdna sequence
I have a sequence of cdna and need to find the name of gene and its organism. I know the blast site but is there any other similar database?
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dark_rider_2010 •
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Hello dark_rider_2010!
Questions similar to yours can already be found at:
We have closed your question to allow us to keep similar content in the same thread.
If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.
Cheers!
Sorry, but are these two mentioned questions similar? Everybody can ask questions with different mails (there is no authentication even!). I just need the answers and didn't do some tricky stuffs :(
Even if multiple accounts would ask the same question those would get closed because of duplicate content.
Those questions look sufficiently similar to me: you still have a fasta file from which you want to find genes and organisms. You got Kraken and Blast as solutions but decided that those don't suffice. This new thread doesn't add additional information compared to the previous threads in my opinion. People tried to help you in the other threads and you didn't follow up on the questions they asked for clarification.
Not exact, I have a ref-seq file. I used trinity to find genes. The result is a fasta file that contains genes. The first thread is about the ref-seq file and the second one is about the output (gene-file). I don't insist on opening or anything similar, I only say that I have a real problem and so hard work to find a very good way to solve it. I have searched all the day and didn't find anything appropriate. I didn't do anything except trying to explain my problem. I also answered to some of the posts and now I see that they are gone! What is the point of closing when you can guide?
So Blast and Kraken don't work? You already received guidance.
The threads are still there...
You also just got another suggestion: C: Recognizing an organism which is combination of other organisms
No, The results of blast site is a result for every gene and I have approximately 800 genes and I don't know how to deal with that. Kraken has just an offline version and the database of it is not updated, on the other hand I couldn't find any paper or any other scientific proof that Kraken is a good tool. I also said that clustering cannot help me, since I have absolutely no idea about the new genome. I told you, I answered all the posts, but now I see that because of my internet connection (maybe), they're not there!