User: shelkmike
shelkmike • 230
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Mikhail Schelkunov
Posts by shelkmike
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2
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95
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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
shelkmike • 230
2
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2
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95
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2
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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
shelkmike • 230
1
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1
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88
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1
answer
... 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 ...
written 24 days ago by
shelkmike • 230
• updated
24 days ago by
Jean-Karim Heriche ♦ 23k
1
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229
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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
shelkmike • 230
1
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0
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229
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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
shelkmike • 230
4
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... 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 ...
written 9 weeks ago by
shelkmike • 230
1
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5
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355
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5
answers
... I recommend UGENE. It is a free and versatile program. ...
written 3 months ago by
shelkmike • 230
0
votes
1
answer
152
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1
answers
... 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
shelkmike • 230
0
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2
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329
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2
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... 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
shelkmike • 230
0
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5
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6.6k
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5
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... 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
shelkmike • 230
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For Phylogeny from incomplete orthogroups
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For A: Criteria for filtering contigs after spades assembly
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