Hi everybody,
I am new with CLC genomics and 454 data. I am working on a non model species (a limpet) so I don't have any reference genome. I did a 454 run on cDNA library (transcriptome). I successfully did a trimming and alignement of the sequences. Now, I would like to blast the contigs against all organisms in NCBI using blastx or blastn to know which genes correspond in these contigs. I would like to know if I can do that directly with the NCBI BLAST available in CLC genomic or if I have to download RefSeq from NCBI to do a local BLAST. I have around 30 000 contigs to BLAST. I know that sometimes, when you blast to many sequences as a batch to NCBI using a software, you can be "black listed" and forbidden to use NCBI (it happened to a searcher from my previous lab who didn't know that before...). So I don't want this to happen... I guess it may depend on the software you use (maybe different ways to submit the batch according to the software, I am not a bioinformatician...)? Please, can you tell me if this is a problem I may have if I blast directly to NCBI using CLC genomic "NCBI BLAST link". If I need to use a local blast, then can you help me to find my way to download the nucleotide database for all organisms (RefSeq). Is it possible to do that in a laptop or I need a server?
Thank you by advance for your help!
All the best
Sophie
I am new with CLC genomics and 454 data. I am working on a non model species (a limpet) so I don't have any reference genome. I did a 454 run on cDNA library (transcriptome). I successfully did a trimming and alignement of the sequences. Now, I would like to blast the contigs against all organisms in NCBI using blastx or blastn to know which genes correspond in these contigs. I would like to know if I can do that directly with the NCBI BLAST available in CLC genomic or if I have to download RefSeq from NCBI to do a local BLAST. I have around 30 000 contigs to BLAST. I know that sometimes, when you blast to many sequences as a batch to NCBI using a software, you can be "black listed" and forbidden to use NCBI (it happened to a searcher from my previous lab who didn't know that before...). So I don't want this to happen... I guess it may depend on the software you use (maybe different ways to submit the batch according to the software, I am not a bioinformatician...)? Please, can you tell me if this is a problem I may have if I blast directly to NCBI using CLC genomic "NCBI BLAST link". If I need to use a local blast, then can you help me to find my way to download the nucleotide database for all organisms (RefSeq). Is it possible to do that in a laptop or I need a server?
Thank you by advance for your help!
All the best
Sophie
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