This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Is There A Library Of Fosmid Sequences?

I want to use a 16S (rRNA) sequence to find if there are any longer (fosmid) reads out there of this species or similar, in an environmental metagenomic context. Querying embl has turned up the 5 I know of though using keywords and filtering for long length.

Is anyone aware of such a database or how to query the common ones for fosmid size (ie >30,000) returns?

UPDATE: Sorry, didnt think! We are looking to see if there is any more homologous sequence data available for a candidate phylum that we have the 16S sequence for, but nothing else.

sequence
• 3,411 views • link
updated by Larry_Parnell Larry_Parnell • written by Daniel Daniel

Which species or phyla in particular do you require? You did not specify this in the question.

• 0 views • link
written by Larry_Parnell Larry_Parnell

2 answers

Some of the early genome sequencing projects used fosmid libraries. One example is the nematode C. elegans. I am not sure if the sister project for C. briggsae also used fosmids. The FCA (flowering control) region of Arabidopsis thaliana chromosome 4 used fosmids. This kind of historical question can be tough and raises the issue of the need for a database describing how genome sequencing projects were designed - the upstream stuff and not just the seq reads and the genes.

• 0 views • link
written by Larry_Parnell Larry_Parnell

Using fosmid as search term at NCBI/nucleotide, 206,570 results were returned. These could be filtered to suit your needs.

• 1 views • link
written by Larry_Parnell Larry_Parnell

The simple ways are the best!

• 0 views • link
written by Daniel Daniel

Log in to answer this question.

More posts like this