User: Benni

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Benni20
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3 weeks, 1 day ago
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2 years, 2 months ago
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b************@web.de

Posts by Benni

<prev • 30 results • page 1 of 3 • next >
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Mass Spectrometry Proteomics: Best methods to find retention time alignment function to match between runs.
... To align multiple LC-MS runs, the retention time has to be transformed to a normalized retention time to make it comparable across runs. What are the current methods used for that? ...
proteomics mass spectrometry written 6 weeks ago by Benni20
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Comment: C: From NCBI Taxonomy to 16s RNA (automated)
... I downloaded the 16S RefSeq Nucleotide sequence records. https://www.ncbi.nlm.nih.gov/nuccore?term=33175%5BBioProject%5D+OR+33317%5BBioProject%5D They contain the information I need. ...
written 3 months ago by Benni20
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Comment: C: From NCBI Taxonomy to 16s RNA (automated)
... 243164 194424 216389 https://www.ncbi.nlm.nih.gov/taxonomy/?term=216389 ...
written 3 months ago by Benni20
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From NCBI Taxonomy to 16s RNA (automated)
... I have a list of NCBI Taxonomy IDs and I want to retrieve the corresponding 16S RNA sequence. I can do this for every single element using SILVA https://www.arb-silva.de/. But I need an automated way. As far as I know, SILVA does not have an REST API, but maybe other databases are accessible in a pr ...
taxonomy 16s rna written 3 months ago by Benni20
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Bioconductor: Retrieve Uniprot Informations with only UniprotKB
... I have a list of UniprotKBs from different organisms and want to be able to retrieve information like the sequence from Uniprot. However, the UniProt.ws package needs me to specify the taxon ID, but I only have the UniprotKB. How can I work around this? ...
bioconductor uniprot written 3 months ago by Benni20
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Align UniRef Cluster for conservation study
... I want to align all sequences from the UniRef cluster "UniRef50_A7ZUK2" to see the conservation of the amino acids. First, is this a good way to investigate conservation? Secondly, how can I download the fasta of "UniRef50_A7ZUK2"? ...
conservation align written 5 months ago by Benni20
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Locus_tag mapping between organisms based on homology
... I basically have two related genomes with their respective locus tag list. Given the locus_tag of organisms 1, I want to find the closest (most homologe) locus_tag available in organisms 2. Including a qualitative measurement of the homology to filter the data. I would prefer homology based on prote ...
homology locus_tag written 6 months ago by Benni20 • updated 6 months ago by h.mon20k
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Annotation Term Overrepresentation/Enrichment Analysis
... I have a gene list with different annotations (GO, KEGG,...) and a gene subset I want to investigate. I tried the onlinetool DAVID to perform an overrepresentation/enrichment analysis, but it doesn´t find my locus tags or uniprot IDs. Since I have the complete Annotation table, I could use this as a ...
annotation kegg go written 6 months ago by Benni20 • updated 6 months ago by n858250
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Predict transcriptional regulation of new genome
... I have the sequence of a Pseudomonas strain. I can predict transcription factors during annotation using EMBOSS. What I'm missing now is the prediction of transcription factor binding sites and the connection between both. I think one way would be: Blast the TF against a curated database of a relat ...
regulation transcription database prokaryote written 7 months ago by Benni20
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Hybrid de novo assembly with Illumina, Sanger and 454
... I have Illumina reads of a bacterial genome and was able to assemble many parts of it. Now I also found Sanger and 454 data for the same strain. Is there a pipeline, that can handle all these data including trimming and error correction? ...
assembly dna sequencing written 8 months ago by Benni20 • updated 8 months ago by h.mon20k

Latest awards to Benni

Popular Question 6 weeks ago, created a question with more than 1,000 views. For Map GO Terms to Protein/Gene of E.coli
Popular Question 6 weeks ago, created a question with more than 1,000 views. For E.coli RNA-seq Gene Expression Collection
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Annotate Protein List with COG / E.coli COG table
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Evaluate Cluster with GO Terms enrichment
Popular Question 3 months ago, created a question with more than 1,000 views. For Evaluate Cluster with GO Terms enrichment
Popular Question 5 months ago, created a question with more than 1,000 views. For Evaluate Cluster with GO Terms enrichment

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