User: piet

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piet1.4k
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Posts by piet

<prev • 183 results • page 1 of 19 • next >
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Answer: A: How to automatically find the right species name when there are typos, using Ent
... You can download a dump of the taxonomy database from NCBI, it is updated several times a day. ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz There is also a REDME file which explains the format of the ASCII files contained in the TAR ball. ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump_ ...
written 7 days ago by piet1.4k
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Comment: C: do blast search using gi numbers
... NCBI is hiding GI numbers from inexperienced kids now, but you can still use them in blast queries and eutils. (see below) ...
written 10 days ago by piet1.4k
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Answer: A: do blast search using gi numbers
... I do not have the cog database installed on my machine, but some tests with blastp instead of rpsblast indicate, that it is neccessary to put every GI number in a separate line: echo 'gi|292833481\ngi|383341230\n' | blastp -task blastp-fast -remote -db nr -outfmt 6 The above command will emit ...
written 10 days ago by piet1.4k
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Comment: C: How can I check the direction of DNA replication?
... The replication complex is a huge protein machinery. It moves from ORI to TER. During its move, both strands are replicated. This is complicated since the mechanisms for the leading and the lagging strand are totally different. However, the overall move of the whole replication apparatus (sometimes ...
written 10 days ago by piet1.4k
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Comment: C: How can I check the direction of DNA replication?
... Your explanation is still lacking important details. Which organismen are you dealing with? Do you know the genomic sequence of the particular isolate you have RNAseqed? I would deduce from your avatar that you are dealing with bacteria. Most eubacteria have circular chromosomes and the location of ...
written 11 days ago by piet1.4k
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Comment: C: Download SRA data via SRA Toolkit.
... What do you want to gain by running it in parallel? This is about downloading 300 SRA files with about 3 gigs each. Bandwidth will be the limiting factor. Also make sure that you have enough free disk space in your HOME or wherever fastq-dump will create its local file cache. ...
written 12 days ago by piet1.4k
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Answer: A: How to get total count of organisms with whole genome sequenced
... The principle problem is how you define the term "complete genome". For most organisms it is still impossible to obtain complete seqences of all replicons in a cell. The outcome of sequencing experiments is limited as well by the method used for nucleic acid extraction as by the sequencing approach. ...
written 3 months ago by piet1.4k
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Comment: C: Multiple fasta sequence query in a single file doing commandline blast
... I would recommend to run the above command with only **one** query sequence first, then with 10 query sequences, and then with 100. How long does it take for one an for 10 queries? Only if all test runs with a small set of queries are successful, you should start with 1000 query sequences. ...
written 3 months ago by piet1.4k
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Comment: C: mapping reads to repetitive elements in genome?
... > bizarre there is nothing bizarre, short reads are just not suited to resolve repeats. You have to use other sequencing strategies like cloning and primer walking if you want to resolve repeats reliably. ...
written 6 months ago by piet1.4k
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Comment: C: spades; Failed to align paired reads
... Spades warns you, that the coverage with K91 is too low. Note that coverage decreases with increasing kmer size. Do not run with large kmers if you do not have enough coverage. ...
written 6 months ago by piet1.4k

Latest awards to piet

Appreciated 12 weeks ago, created a post with more than 5 votes. For A: Fastest way from SRA to fastq PE reads
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Howto use NCBI programs behind a HTTP proxy
Supporter 10 months ago, voted at least 25 times.
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How to determine if a bacterial de-novo assembly is a new species
Guru 12 months ago, received more than 100 upvotes.
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: How to determine if a bacterial de-novo assembly is a new species
Scholar 14 months ago, created an answer that has been accepted. For A: NCBI E-utilities : HTTP POST not working for EPost
Centurion 14 months ago, created 100 posts.
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: How to determine if a bacterial de-novo assembly is a new species
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: How to determine if a bacterial de-novo assembly is a new species
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: How to determine if a bacterial de-novo assembly is a new species
Appreciated 17 months ago, created a post with more than 5 votes. For A: Fastest way from SRA to fastq PE reads
Scholar 17 months ago, created an answer that has been accepted. For A: NCBI E-utilities : HTTP POST not working for EPost
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: How to determine if a bacterial de-novo assembly is a new species
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: Python Programming (Suggestions are needed)
Scholar 17 months ago, created an answer that has been accepted. For A: NCBI E-utilities : HTTP POST not working for EPost
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: How to determine if a bacterial de-novo assembly is a new species
Scholar 18 months ago, created an answer that has been accepted. For A: NCBI E-utilities : HTTP POST not working for EPost
Scholar 21 months ago, created an answer that has been accepted. For A: NCBI E-utilities : HTTP POST not working for EPost
Scholar 2.1 years ago, created an answer that has been accepted. For A: NCBI E-utilities : HTTP POST not working for EPost
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: How to determine if a bacterial de-novo assembly is a new species

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