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-   -   shotgun sequencing dataset (http://seqanswers.com/forums/showthread.php?t=61793)

Heena Farooq 08-07-2015 02:49 AM

shotgun sequencing dataset
 
Please send me the shotgun sequence dataset of 27 million sequencing reads in fasta format so that i can find out the genes from that sequence. thanks in advance!!! if possible, can anyone send me a link for downloading celera generated shotgun sequence.

GenoMax 08-07-2015 04:04 AM

Unless you provide some additional information you are not going to get meaningful help.

Why 27 million and why fasta format? You don't care about what organism the data is from?

Heena Farooq 08-07-2015 08:07 AM

Actually i have read the paper namely "Whole genome shotgun assembly and comparison of human genome assemblies". and i need to use its dataset which is generated from celera in 2001 called shotgun dataset which is of 27 million sequencing reads and i need to review this paper by calculating its accuracy of gene prediction. but i am not able to find its dataset's dna sequence so that i can find genes from that. Please help me out.

GenoMax 08-07-2015 08:15 AM

I assume you are referring to this paper: http://www.pnas.org/content/101/7/1916.full

Quote:

Abbreviations: WGSA, whole-genome shotgun assembly; CSA, compartmental shotgun assembly; WGA, whole-genome assembly.

Data deposition: The sequences of the assemblies herein referred to as WGSA, CSA, and WGA have been deposited in the GenBank database (whole-genome assembly project accession nos. AADD00000000, AADC00000000, and AADB00000000).

If so the projects in that paper can be found here (these links seem to now point to the current versions of the human genome though):

http://www.ncbi.nlm.nih.gov/genome/?term=AADD00000000
http://www.ncbi.nlm.nih.gov/genome/?term=AADC00000000

Third one does not seem to be in GenBank (AADB00000000).

Heena Farooq 08-07-2015 10:12 AM

yes, exactly...you are getting me right..that one is the paper.. i am new in this field hope u dnt mind. e.g. AADC00000000 contains a number of sequences means it has 169156 contigs. can you please tell me which sequence i need to use and how can i use it? thanks for your concern and please help

GenoMax 08-07-2015 10:32 AM

It is not clear as to what you are trying to do.

A set of genes was predicted in early 2000's based on the first assembly of human genome but that number has been shrinking over the years (see: http://www.the-scientist.com/?articl...Shrinks-Again/).

Current human genome contains fairly well organized chromosome sequences which you can download from this link (in fasta format):ftp://ftp.ncbi.nlm.nih.gov/genomes/a...genomic.fna.gz

I am not sure where you see 169156 contigs? Earliest dataset I can see on UCSC is from May 2010: http://hgdownload.soe.ucsc.edu/golde...y2000/bigZips/

Heena Farooq 08-07-2015 11:12 AM

Ok let me explain you.. i have to find out the mutated genes.. and for that i have to take dataset..and thats y m reading the previous mentioned paper (1916.full).. m tryng to take dataset contains disease causing genes and dataset contains whole human genome.. aftr that i vl find out mutated genes frm thse two.. nw i gt ur dataset which you mentioned above..bt i m getting confusd abt its sequence..tht wt shud i use.. and u can also see 169156 contigs as locuslength of dataset AADC00000000.. above all this, if u dnt mind can you give me the direction for doing the same process which i want to do..hpe u undrstd wel nw..thanks

Heena Farooq 08-14-2015 06:41 AM

please send me the algorithm for GeneZilla gene finder algorithm...i will be thankful to you...


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