User: Pablacious

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Pablacious610
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Posts by Pablacious

<prev • 33 results • page 1 of 4 • next >
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Comment: C: Mapping Rosetta/Merck Human 44k 1.1 microarray to IlluminaHT-12 v3 probes
... Hi David, did you get anywhere on this? I'm trying to find the probe sequences for that array unsuccessfully, would you have any clues I could use? Thanks! ...
written 9 months ago by Pablacious610
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Comment: C: Create Instances From Position Frequency Matrix
... Why would you want to search for a random instance of the motif instead of the whole motif? Using the motif to search is more sensitive than an instance. ...
written 5.4 years ago by Pablacious610
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Answer: A: Refseq (.Fna) Vs. (.Gbff) Files
... The > line in a fasta file is only divided in the identifier part and the description part. The identifier part goes between the > and the first space. Whatever goes after the first space is the description part (which can have all the spaces that you want), so there is no such a thing as a la ...
written 5.4 years ago by Pablacious610
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Answer: A: Go Enrichment From Protein Id
... For E. coli I would use EcoCyc from SRI. It is probably one of the most comprehensive and curated resources when it comes to E. coli. It has a module for doing enrichment analysis through its smart tables, see here http://ecocyc.org/PToolsWebsiteHowto.shtml#node_toc_node_sec_7.5.1 It might be more ...
written 5.4 years ago by Pablacious610
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Answer: A: How Do You Find The Available Number Of Insect And Metazoan Genomes?
... I would use the NCBI Taxonomy, where you can select a particular taxonomic domain and then switch on the counts of available genomes, publications, etc. Go to http://www.ncbi.nlm.nih.gov/taxonomy/?term=insects click on Hexapoda and then on the grey rectangle full of check boxes choose what you wa ...
written 5.4 years ago by Pablacious610
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Equivalent Of Ensembl Gene Regulatory Build For Fly (Fruitfly)
... Dear community, I'm interested in fetching transcription factor binding sites (the actual locations in the genome) for the upstreams of certain genes in Drosophila melanogaster (fruit fly). ENSEMBL doesn't have a gene regulatory build for fly, as it does for human or mouse. Is anyone aware of a res ...
transcription-factor ensembl written 5.4 years ago by Pablacious610
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Answer: A: Find Genes In Coral Genomes For Building A Phylogenetic Tree Of A Gene'S Evoluti
... Regarding point 2, you probably want to use protein alignments instead of gene based alignments, unless that your species are very close in phylogenetic terms. Regarding point 3, I would recommend you to use the strategy used at ENSEMBL to build your gene trees: http://www.ensembl.org/info/genome/c ...
written 5.7 years ago by Pablacious610
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Comment: C: Extracting Genbank Features With Biojava3 Or Java Library
... Currently there doesn't seem to be a way of parsing genbank files with biojava3. The only mention of genbank in the whole project seems to be in the DataSource class and some tests that use it (looking at the git project). There is nothing that seems related in the API either. There is a thread in o ...
written 6.3 years ago by Pablacious610
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Comment: C: Beginner Blasting Short Sequences
... You could also use "water" from the EMBOSS package (another Smith-Waterman algorithm implementation). Totally agree on avoiding the heuristics for data sets of this size. ...
written 7.3 years ago by Pablacious610
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Comment: C: Are There Any Tools For Ontology Enrichment Analysis That Work With Any Ontology
... Thanks Andrew, this looks promising. ...
written 7.6 years ago by Pablacious610

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Popular Question 4.0 years ago, created a question with more than 1,000 views. For How To Retrieve The Crossreferences To Other Databases From Pubchem Compounds
Popular Question 5.1 years ago, created a question with more than 1,000 views. For How To Retrieve The Crossreferences To Other Databases From Pubchem Compounds
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: Locating Motif Within A Protein Sequence
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: How To Convert A Big Fasta File With Multi-Line Dna Sequences Into A Fasta File
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Appreciated 5.4 years ago, created a post with more than 5 votes. For A: A List Of Regular-Expressions For Recognizing Ids From Various Databases
Scholar 5.4 years ago, created an answer that has been accepted. For A: Find Genes In Coral Genomes For Building A Phylogenetic Tree Of A Gene'S Evoluti
Teacher 7.7 years ago, created an answer with at least 3 up-votes. For A: How To Convert A Big Fasta File With Multi-Line Dna Sequences Into A Fasta File
Student 7.7 years ago, asked a question with at least 3 up-votes. For How Would You Classify Small Molecules Into Biologically Meaningful Categories?
Good Answer 7.8 years ago, created an answer that was upvoted at least 5 times. For A: A List Of Regular-Expressions For Recognizing Ids From Various Databases
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Appreciated 7.8 years ago, created a post with more than 5 votes. For A: A List Of Regular-Expressions For Recognizing Ids From Various Databases
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Appreciated 7.8 years ago, created a post with more than 5 votes. For A: Is There Any Publicly Available Documentation About Velvet'S Source Code?

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