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I am not a biologist. Please pardon me, if my question does not make sense.

I am trying to obtain a DNA sequence for pattern analysis in Matlab. I used to generate random sequence randseq in Matlab. However, I am trying to obtain some real dataset.

Any idea where I can obtain the DNA dataset. I am looking at a dataset having acgt patterns

Thanks

EDIT : Thanks a lot guys, I found it here. : http://www.ncbi.nlm.nih.gov/nucest?term=((human%5BComponent+Accession%5D)+AND+normal+Breast+gene+sequence)+AND+1000%3A10000%5BSequence+Length%5D

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4 Answers 4

up vote 8 down vote accepted

There are several nucleotide sequence datbases available. One of the largest is the NCBI GenBank at http://www.ncbi.nlm.nih.gov/genbank/

You may use the search bar at the top to search for nucleotide sequences belonging to a certain organism or gene. For example, searching for "E coli" will give you the full genome sequences for several bacterial species, with a strain of E. coli as the top result. The E. coli genome is about 5 MB large. If you want a single gene sequence, searching for "sonic hedgehog" (without quotes) will return the human hedgehog gene as the top result, which is 1,481 basepairs long.

To get a sequence in raw format, select "FASTA" below the entry. At the page you get sent to , chose "send" in the upper right corner and under "Choose destination", "file". This will give you a .fasta file, the standard raw sequence format. The first line, starting with ">" will be metadata, while the rest of the file consists of the nucleotide letters only.

Note that in addition to a,t,g and c, you may also find other characters, most often "n". These characters describe ambiguity in the sequence (meaning that the nucleotide at that position could not be determined). For a full description of the FASTA format sequence representation, see http://en.wikipedia.org/wiki/FASTA_format#Sequence_representation

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Thanks a lot for your help –  www.sapnaedu.in Mar 6 at 8:36
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@www.sapnaedu.in Hi! If you find that this post answered your question well, you can accept this as the answer by clicking the checkmark. –  biogirl Mar 7 at 5:37
    
You guys are the best. You are so unlike the IT guys. :) Always there to help. –  www.sapnaedu.in Mar 7 at 11:06

Try Wolfram|Alpha at www.wolframalpha.com. On the home page is Examples. Click it. One of the boxes on the next screen is Life Sciences. Within that box is a choice of Human genome. Click on that. You will then see examples of searches. Those include sections of the human genome and even sequences for specific genes. Choose an existing one or modify. Then submit the query clicking on the = at the right hand side of the (sample) query. When you get a result from such a search, mouse over the ATGC sequence and you will see a menu appear. The icon "A" allows you to copy the plaintext. That should quickly give you sample sequences for further processing.

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Since you don't seem to care what sequence you have as long as it is a real sequence, here's the (one of them anyway) mRNA sequence of the human tumor suppressor TP53, perhaps the most studied gene in the world:

http://www.ncbi.nlm.nih.gov/nuccore/371502115?report=fasta

If you prefer genomic sequences as opposed to mRNA:

http://www.ncbi.nlm.nih.gov/nuccore/383209646?report=fasta&from=5001&to=24149

And if you are looking for a larger sample size, here's the entire sequence of the human 22nd chromosome (careful, largish file, ~30MB)

http://www.ncbi.nlm.nih.gov/nuccore/568801965?report=fasta

Finally, if you want a lot of sequence, you can download the entire human genome from here (careful: 905MB):

ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz

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No, I do, I am looking for a very particular pattern from humans suffering from cancer. Thanks a lot –  www.sapnaedu.in Mar 6 at 15:28
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@www.sapnaedu.in huh? What pattern? You don't mention anything like that in your question. The sequences you are using are not from cancer, do you want sequences from cancer patients? –  terdon Mar 6 at 15:32
    
Yes, I am sorry, I was not aware of it earlier. Now that I am able to find the sequences, I am particularly looking for patterns from Humans suffering from cancer. –  www.sapnaedu.in Mar 6 at 15:40
    
@www.sapnaedu.in please explain what you are actually trying to do. There are hundreds or thousands of available cancer datasets but which one is good for you will depend on the analysis you will perform. Most sequences will be identical in cancer and healthy tissue. If you want to find patterns characteristic of cancer you will need to be more specific. –  terdon Mar 6 at 15:42
    
I am really sorry, I donot have much information to share apart from what I have already mentioned. I will post it later once I have it. –  www.sapnaedu.in Mar 6 at 15:46

you can download real sequences from GENBANK. You can search model organism(s) or genetic marker(s) and download it in *.fasta or other format. Good luck!

http://www.ncbi.nlm.nih.gov/genbank/

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Searching the database was really complicated. Thanks a lot for your support. –  www.sapnaedu.in Mar 6 at 8:35

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