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How to download the complete list of genes in a chromosome(chromosome 19)


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#1 manshal

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Posted 22 September 2010 - 11:03 AM

I am trying to find complete list of genes in chromosome 19 and chromosome 20. I tried to do it in NCBI map viewer, I got the following results stating that it had 1992 genes http://www.ncbi.nlm....tg-r,ugHs,genes[1.00%3A59128983.00]&CMD=TXT#1

The above link is only displaying 1000 and 1500 can be downloaded, For complete list it is asking to go to ftp site, which is very confused. Can someone please help me for complete data

Thanks in advance

manshal

#2 pcrman

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Posted 22 September 2010 - 01:18 PM

BioMart is the best tool for gene information retrieval and allows for almost any kind of downloading. http://www.biomart.o...omart/martview/

To start, choose a database such as Ensembl Genes 59, -> Dataset (organism) -> Filters -> Chromosome 19 -> ...

#3 manshal

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Posted 22 September 2010 - 01:45 PM

BioMart is the best tool for gene information retrieval and allows for almost any kind of downloading. http://www.biomart.o...omart/martview/

To start, choose a database such as Ensembl Genes 59, -> Dataset (organism) -> Filters -> Chromosome 19 -> ...



Thank you so much. That was great. I had one more question.

I know that ensembl lists the exons and intron boundaries, what would be the best way to download the intronic sequences. I am trying to list all the intronic material in the chromosome, for that I thought the best way would be list all genes in a particular chromosome and then separate the exon and introns in each genes. is that good idea? if so, can you please tell me how to download the nucleotide sequences( the site only lists the boundaries) . Please let me know

Thanks in advance

Manshal

#4 HomeBrew

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Posted 22 September 2010 - 04:02 PM

Try here.

#5 pcrman

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Posted 22 September 2010 - 05:46 PM

how to download the nucleotide sequences( the site only lists the boundaries)


One the left, click Attributes, then on the main page, check "Sequences", in the area immediately below you can choose which region to download. However, there seems to not have the option of downloading only intronic sequences.

#6 manshal

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Posted 23 September 2010 - 09:24 AM

Try here.


Thanks for taking time to reply... but I am little confused over the link..I tried to open the links on the website you gave.. but i think it contains sequences from different chromosomes, and one more thing, what does that list contain? I see that they are all genes from different chromosomes?

Please let me know, I am a novice in this study, just trying to learn basics

Thanks in advance

Manshal

Edited by manshal, 23 September 2010 - 09:35 AM.


#7 manshal

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Posted 23 September 2010 - 10:01 AM

how to download the nucleotide sequences( the site only lists the boundaries)


One the left, click Attributes, then on the main page, check "Sequences", in the area immediately below you can choose which region to download. However, there seems to not have the option of downloading only intronic sequences.

Yeah that is working for exons but not introns... is there any software in which you can input whole DNA sequence(which includes introns and exons) and it separates the exons and introns. Please let me know

Thanks
Manshal

#8 manshal

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Posted 23 September 2010 - 04:21 PM

Hello All

I am trying to download all the genes in a chromosome. For that I went to NCBI map viewer.
http://www.ncbi.nlm....xid=9606&chr=19

After that in the data below, there is Map 4 with total number of genes in the sequence. I clicked on Table view, which shows first 1000 genes, but I need all of them. it also says first 1500 available for download, but I need all 1992 genes.It says for all sequences .. go to ftp site.. which is very confusing... Can someone please help me with that?? .I would greatly appreciate it

Someone from this forum told me to go to biomart for the download of any genomic sequences.. but.. that site only displays exons.. but not introns.. but when you do the search with the NCBI gene IDs , they does show introns. So please someone I need the list of genes with NCBI gene ID's.

Thanks
Manshal




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