User: hodayabeer

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hodayabeer10
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2 years, 7 months ago
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Posts by hodayabeer

<prev • 10 results • page 1 of 1 • next >
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How to define blast online to filter out PREDICTED and hypothetical proteins
... Hi, I am trying to blast some proteins using 'blastp' vs. some organisms using the Non- redundant protein sequences database (nr) I have found a [solution][1] that is applicable only for blastn by using an Entrez Query of: all[filter] NOT predicted[title] but unfortunately it doesn't work and I sti ...
blastp written 9 months ago by hodayabeer10 • updated 9 months ago by Mensur Dlakic4.2k
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Error in BioMartVersion
... Hi, I am trying to convert between EntrezID to gene symbol using 'bioMart' package and the following function: source("https://bioconductor.org/biocLite.R") library('EnrichmentBrowser') library('biomaRt') convert_to_genes_symbol<-function(ptwy_genes){ library('Enrichm ...
gene R biomart gene symbol entrezid written 2.2 years ago by hodayabeer10 • updated 2.2 years ago by James Ashmore2.8k
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Comment: C: hierarchial clustering of genes- identify number of clusters
... Thank you for your answer. What I am trying to do is to write a code that will identify number of clusters in a lot of datasets, simultaniously. Therefore, I am trying to find a systematic way to do that, without the involvment of human. So how can I apply your suggestion in a R code, and let the a ...
written 2.2 years ago by hodayabeer10
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hierarchial clustering of genes- identify number of clusters
... Hi all, I have a data set where the rows are genes and columns are phylogenetic profiling scores. I clustered this dataset of genes in Hierarchial Clustering in R, and got a dendogram of the hclust() output. I need to identify the number of clusters, so that genes in the same cluster will be very ...
gene hierarchial clustering cluster R written 2.2 years ago by hodayabeer10 • updated 2.2 years ago by Kevin Blighe56k
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Comment: C: How to prevent blastp from aligning small parts of query sequence and scoring th
... how can I extract only the results where the alignment lengths is equal or close to the query / subject length? ...
written 2.5 years ago by hodayabeer10
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Comment: C: How to prevent blastp from aligning small parts of query sequence and scoring th
... how can I extract only the results where the alignment lengths is equal or close to the query / subject length? ...
written 2.5 years ago by hodayabeer10
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Comment: C: How to prevent blastp from aligning small parts of query sequence and scoring th
... but I want to get only full alignments of the query sequence ...
written 2.5 years ago by hodayabeer10
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How to prevent blastp from aligning small parts of query sequence and scoring that high?
... Hi, I was blasting proteome of yeast against a large database of Archaea. Something is wrong with the results because I got too large P Identity for too much proteins. I assume that the problem is that blast scores small parts of the query sequence once it found an alignment to that, and therefore ...
alignment sequence blast written 2.5 years ago by hodayabeer10
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Comment: C: Scientific Names In Blast Output And Databases
... Hi, I was facing the same problem and then I realized that the blast command must be in the same directory as the nr database and the 2 taxdb files (.bti , .btd). It solved the problem. Good luck! ...
written 2.6 years ago by hodayabeer10
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Comment: C: Species identification via gilist
... Hi Yi-Ting, can I ask how did you get this bacteria gi list from? I am trying to download it directly from the NCBI (by 'save to file' -> GI List etc...) but it failes due to timeout error.. Do you have an easy way to do that? tnx in advance ...
written 2.6 years ago by hodayabeer10

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