Question on the logic of my search query

[William Chow]

Hi,

I was wondering if someone can help me see if this is even possible using the portal (I've looked through the documents and searched the forum but I can't find anything, or may not be looking in the right place).

Goal: Find all the underlying parent contigs/scaffolds/genomes from metagenomes(or all source data) that contain a collection of PFAMs and download the assembled sequence or even raw reads.

Would this be the best way to approach this?

1. Use scaffold search, and advanced search builder, to search all isolates (all, drafts, assembled etc) for a bunch of pfam ids. 

• Does this retrieve ALL contigs from metagenomes ?
• On the portal it does say there are limits, and/or very slow query, is there a faster way to accomplish this?

2. Given the results of the scaffold list, use DownloadingIMGSequenceandAnnno instructions to download.

Is that the best way to do it, or am I missing some API service that can do the same?  I am primarily interested in sequence information not found in the other public databases (refseq etc)