User: Peter

gravatar for Peter
Peter90
Reputation:
90
Status:
Trusted
Location:
European Union
Last seen:
3 years, 2 months ago
Joined:
8 years, 10 months ago
Email:
p******@gmail.com

Posts by Peter

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Extracting subalignments from MAF file
... Have a look at https://github.com/bxlab/bx-python ...
written 3.2 years ago by Peter90
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Comment: C: Filter Bacterial sequences from Metagenomics
... Kaiju will work with only 50GB RAM. You can also use the [web server][1] and upload your reads there for taxonomic classification. [1]: http://kaiju.binf.ku.dk/ ...
written 3.4 years ago by Peter90
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Comment: C: How To Avoid False Negative And False Positive When Searching For Tfbs?
... Yes exactly this is the problem. However you can try to optimize your specificity by comparative analysis (e.g. only consider predicted binding sites that you find in mouse and rat and maybe others) ...
written 8.9 years ago by Peter90
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Answer: A: Fasta Alignment Format - Sequences Must Be Same Length?
... Yes, alignment programs usually output alignments with equal-length sequences. Of course, if you align two sequences with different lengths, gap characters will be introduced (global alignment) ...
written 8.9 years ago by Peter90
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Comment: C: Phylogenetic Analysis Of Whole Genomes
... I would try to use the "fasttree" program, it gives comparable results to PhyML but is much faster, which would be beneficial on a genome wide scale. Anyway, if you use multiple loci of whole genomes for phylogeny reconstruction, there would be only a very tiny difference between different programs. ...
written 8.9 years ago by Peter90
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Answer: A: What Non Coding Genes Have Introns?
... Ribosomal RNAs frequently have introns. ...
written 8.9 years ago by Peter90
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Answer: A: What Are The Classic Papers In Bioinformatics?
... Ruth Nussinov and George Pieczenik and Jerrold R. Griggs and Daniel J. Kleitman: Algorithms for Loop Matchings. In: SIAM Journal on Applied Mathematics. 35, Nr. 1, Juli 1978, S. 68-82. 30 years ago, she came up with a beautiful dynamic programming algorithm for secondary structure prediction. ...
written 8.9 years ago by Peter90

Latest awards to Peter

Appreciated 8.8 years ago, created a post with more than 5 votes. For A: Fasta Alignment Format - Sequences Must Be Same Length?
Teacher 8.8 years ago, created an answer with at least 3 up-votes. For A: What Are The Classic Papers In Bioinformatics?
Teacher 8.8 years ago, created an answer with at least 3 up-votes. For A: Fasta Alignment Format - Sequences Must Be Same Length?

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