Easiest Way To Obtain Chromosome Length?

Question

[Sequer]

Was just wondering contrary to a longer way. What is the easiest way for example to get a Drosophila melanogaster or any other organism's chromosome length?

Answer 1

[Pierre Lindenbaum]

As you cannot get the length of the longest chromosomes, I suppose that there is no such database.

The ucsc stores this information in the mysql table chromInfo for a few organisms.

$ mysql  --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e 'select chrom,size from chromInfo limit 5'
+-------+-----------+
| chrom | size      |
+-------+-----------+
| chr1  | 249250621 |
| chr2  | 243199373 |
| chr3  | 198022430 |
| chr4  | 191154276 |
| chr5  | 180915260 |
+-------+-----------+

Answer 2

[Casey Bergman]

The UCSC browser provides a summary page of chromosome lengths for each of the genomes in their database, e.g. for D. melanogaster (release 5/dm3): http://genome.ucsc.edu/cgi-bin/hgTracks?db=dm3&chromInfoPage=

Just swap the db=xx for another genome.

Answer 3

[Ian]

You can also use UCSCs fetchChromSizes script.

[Casey Bergman]

I knew their was a Kent utility to do this but couldn't find it this AM. Thanks Ian.

Answer 4

[Gareth Palidwor]

Remember that the lengths you get from the model can have various biases. For example: there are 3 million N's added to each end of mouse and human assembly chromosomes (except chrY) to represent telomeres. These are conventions and not necessarily representative of "real" telomere length. This should be kept in mind when you're doing any sort of length related analysis.

[Casey Bergman]

Good point Gareth.

Answer 5

[Tommy Carstensen]

If your system doesn't have mysql as suggested by Pierre, then you can do (as suggested by Pierre in another thread):

curl -s ftp://hgdownload.cse.ucsc.edu/goldenPath/$db/database/chromInfo.txt.gz | gunzip -c

$db could for example be hg19:

curl -s ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz | gunzip -c