Hello
I am a newcomer to bioinformatics, and need your assistance.
I bought CLC Genomics Workbench, and started with using BLAST at NCBI.
I selected CLC's tutorial dataseet (P. aeruginosa) and
chose Limit by entrez query as Bacteria [ORGN] or Viruses [ORGN].
However, the process expired after half an hour,
and returned only an error message.
I contacted the supplier of CLC, who replied that NCBI recently rejects (or put a very low priority to) requests through CLC workbench. The supplier recommended me to use "Download BLAST Databases" tool.
My ultimate interest is virus. My idea is
first exclude reads which align with human genome
then denovo assemble the remainiing reads
and align the resulting contigs (scaffolds) to known bacteria/viruses.
Non-aligned contigs would be from a novel virus.
Please let me know
which bacterial/viral database (with URL) I have to download.
I would like to download not only NCBI DB but also GOLD database
which includes non-published sequences.
Thank you
I am a newcomer to bioinformatics, and need your assistance.
I bought CLC Genomics Workbench, and started with using BLAST at NCBI.
I selected CLC's tutorial dataseet (P. aeruginosa) and
chose Limit by entrez query as Bacteria [ORGN] or Viruses [ORGN].
However, the process expired after half an hour,
and returned only an error message.
I contacted the supplier of CLC, who replied that NCBI recently rejects (or put a very low priority to) requests through CLC workbench. The supplier recommended me to use "Download BLAST Databases" tool.
My ultimate interest is virus. My idea is
first exclude reads which align with human genome
then denovo assemble the remainiing reads
and align the resulting contigs (scaffolds) to known bacteria/viruses.
Non-aligned contigs would be from a novel virus.
Please let me know
which bacterial/viral database (with URL) I have to download.
I would like to download not only NCBI DB but also GOLD database
which includes non-published sequences.
Thank you
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