User: Benni

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Benni20
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1 year, 9 months ago
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Posts by Benni

<prev • 25 results • page 1 of 3 • next >
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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 4 weeks 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 5 weeks ago by Benni20 • updated 5 weeks ago by h.mon15k
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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 weeks ago by Benni20 • updated 6 weeks 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 11 weeks 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 3 months ago by Benni20 • updated 3 months ago by h.mon15k
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Short-read genome assembly with related reference genome
... I have paired-end Illumina data of a bacteria (1) and a reference genome of the same bacteria (2). However, the reference bacteria is not the same as (1), because (1) was treated differently and changed it`s genome. Now I want to assemble the genome of (1) using the reference genome, since de novo a ...
illumina ngs sequencing assembly written 3 months ago by Benni20 • updated 3 months ago by jean.elbers210
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Coverage of 320; Would it be useful to perform very stringent filtering?
... I have Illumina data of a 6Mb bacteria. Insert length = 400, read length = 151, estimated coverage = 320 (read length * #sequences / 6Mb). I think I don´t need to use all the data. I could randomly sample 25% or so. But I could also filter sequences very stringent based on quality. Do you think it w ...
assembly ngs bacteria written 3 months ago by Benni20 • updated 3 months ago by Macspider2.4k
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Data on translational efficiency of genes in e.coli?
... I´m searching for existing data on translational efficiency of genes in e.coli. The efficiency is influenced by the codon bias, the Shine-Dalgarno sequence etc.. Maybe there is simulation data or even experimental data? The best case would be a numerical value for each gene. I also search for mRNA- ...
translation e.coli written 13 months ago by Benni20
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Comment: C: Annotate Protein List with COG / E.coli COG table
... EcoCyc doesn´t support COG annotation. How do I get the table in .csv and not .html? ...
written 13 months ago by Benni20
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Annotate Protein List with COG / E.coli COG table
... I have a protein list of escherichia coli. I want to annotate this list with the COG terms. Is there an online tool for that or is there a way to get a annotated gene/protein list for e.coli? I don´t want to run a sequence blast, since there should be already a database for e.coli proteins? ...
cog written 13 months ago by Benni20

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