User: shelkmike

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shelkmike230
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Russian Federation
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5 years, 10 months ago
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Mikhail Schelkunov

Posts by shelkmike

<prev • 30 results • page 1 of 3 • next >
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Comment: C: BlastP vs BlastX
... The reference is simply the list of options of BLASTX. If you run "blastx -help", you'll see, among other options, the option "-strand" with the following description: "Query strand(s) to search against database/subject. Default = both". Also, there is a format specifier "qframe", which shows the qu ...
written 24 days ago by shelkmike230
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Answer: A: BlastP vs BlastX
... No, they are not the same. BLASTX performs translation in all 6 reading frames and aligns all of them to the database. If you translate your gene into a protein and run BLASTP, then only one (the correct one) reading frame will be used. ...
written 24 days ago by shelkmike230
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Tool to find double strand breaks
... Hi everyone Does anyone know a tool to find double strand breaks from a read mapping? They cannot be simply found by coverage drops, because bases to the left and to the right from the break can be covered by quite a lot of reads. Double strand breaks can be found by the absence of reads that span ...
variant calling double strand breaks written 24 days ago by shelkmike230 • updated 24 days ago by Jean-Karim Heriche23k
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Comment: C: Elloreas, a new genome assembler
... After every iteration Elloreas checks whether there is a long overlap between the 5' and the 3' ends. If such an overlap exists and has a sequence similarity of 100%, then Elloreas stops and tells the user that the genome has probably circularized. ...
written 9 weeks ago by shelkmike230
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Comment: C: Elloreas, a new genome assembler
... Yes, I know MASURCA. MASURCA is very different from Elloreas. For example, MASURCA is a de novo assembler, while Elloreas was designed first and foremost for local assembly. ...
written 9 weeks ago by shelkmike230
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Tool: Elloreas, a new genome assembler
... Hi everyone I've created a new genome assembler named Elloreas (an abbreviation for ELongating LOng REad ASsembler). Simply speaking, it works in the following way: 1) You provide it with a starter. It can be a contig from some other assembly or just a random read. 2) It maps reads to the 3' end of ...
assembly next-gen tool written 9 weeks ago by shelkmike230
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Answer: A: windows bioinformatics programs
... I recommend UGENE. It is a free and versatile program. ...
written 3 months ago by shelkmike230
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Answer: A: Go enrichment analysis- blastp uniprot
... I recommend to use PANNZER2 for GO annotation. It is a high quality program which works faster than Blast2GO. For GO enrichment I recommend GOATOOLS - it is quite simple but efficient. ...
written 3 months ago by shelkmike230
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Answer: A: Do all samples in SRA have a corresponding sample in BioSample?
... According to the rules of NCBI, it is mandatory for each SRA submission to have a registered corresponding BioSample: "Registering project and biological samples at the NCBI BioProject and the BioSample databases is a prerequisite for any public SRA submission" (https://www.ncbi.nlm.nih.gov/sra/docs ...
written 9 months ago by shelkmike230
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Comment: C: Lossless ALAPY Fastq Compressor (now for MacOS X with 10-20% improved speed and
... First of all, thank you. ALAPY compressor has helped our laboratory to reduce the size of sequencing reads made by our HiSeq a lot. What I want to ask: could you please make an option to decompress many files by one command? Like "alapy_arc -d *.ac" instead of "alapy_arc -d some_single_file.ac". It ...
written 16 months ago by shelkmike230

Latest awards to shelkmike

Voter 6 months ago, voted more than 100 times.
Popular Question 7 months ago, created a question with more than 1,000 views. For Phylogeny from incomplete orthogroups
Scholar 17 months ago, created an answer that has been accepted. For A: Criteria for filtering contigs after spades assembly
Popular Question 19 months ago, created a question with more than 1,000 views. For Is BUSCO really better than CEGMA for genome assembly quality evaluation?
Scholar 2.5 years ago, created an answer that has been accepted. For A: Criteria for filtering contigs after spades assembly
Supporter 3.8 years ago, voted at least 25 times.

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