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Download Homo sapiens, Lymphoma ESTs and make database on Bio Linux OS.

Dear Sir/Madam, I want to download all EST files of Homo sapiens Lymphoma associated nucleotides from NCBI and then need to convert them all into database, for that, what should I do and what are the codes that I need to do in python language in Bio Linux? I would like to know the all steps.

fasta est download bio-linux
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written by Sashinika • Sashinika
  1. Please explain what you mean by "Human Lymphoma associated nucleotides"
  2. Please give us an example of how you can find one EST entry for the above term
  3. How do you perform a search for ALL EST entries for that term?
  4. What do you mean by "build a database"?
  5. Why do you need to use Python?

Above all, how did you come up with this problem statement? Was it given to you by someone else?

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written by Ram Ram

Dear Sir, I am doing my very first research on Bioinformatics and my topic is related to in silico identification of miRNAs that are associated with Lymphoma genes in humans. Lymphoma is cancer. So I need to clarify some problems related to python coding on Bio-Linux and building a database on Bio-Linux to come up with the results. Here are the answers to your questions

  1. Those are the keywords that I need to download from the NCBI database. Human Lymphoma means Cancer. So its associated genes are available in the body. that genes have nucleotides. Those nucleotides' EST sequences are available in the NCBI database. so I need to download them from the database NCBI.
  2. In the NCBI database txt box, should select the nucleotides and need to enter the search bar as "homo sapiens lymphoma est" and search. then will obtain the sequences. then need to select one seq and click the drop-down button of the " send to" txt. then will receive a message box and in that, click on complete record, then click on the file, then select FASTA for the format, given default order and finally create file. then will obtain the downloaded sequence notepad file, sir. That is what I did to obtain est entry.
  3. I have to download sequences one by one sir. otherwise cannot be recognized the particular sequence for each BLAST.
  4. To perform BLAST N on Bio-Linux I need to convert the sequence set into the database on Bio-Linux OS. So that is why we need to build a database.
  5. All the processes of in silico identification of miRNA will carry out in the Bio-Linux OS sir. fo that needs to use coding in Python Language
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updated by Ram Ram • written by Sashinika • Sashinika

There are a whole lot of assumptions in your statements above that are quite naive. Please get in touch with an experienced bioinformatician and, if possible, an experienced lymphoma researcher and explain your premise to them and listen to their feedback.

For example, your statement about genes associated with lymphoma being available on NCBI is vaguely true, but how do you determine how each gene is associated with Lymphoma specifically? Also, when you search for "homo sapiens lymphoma est", how are you sure that all returned results are relevant to your area of research? What if a result matched "homo sapiens est" but not "lymphoma"? It sounds trivial, but it could be a huge factor. You need to get in touch with a bioinformatician that you can meet in person.

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written by Ram Ram

Dear Sir Thank you very much for your feedback. okay, I will just try to do it the way, which you have told me above. Yes, I can understand the things that you have said to me. again thanks a lot sir.

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written by Sashinika • Sashinika

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