User: carina2817

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carina281710
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Posts by carina2817

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Comment: C: Which software is suitable for protein prediction from whole eukaryotic genomes?
... The gff file looks like this: gff-version 3 !gff-spec-version 1.21 !processor NCBI annotwriter !genome-build ASM263302v1 !genome-build-accession NCBI_Assembly:GCA_002633025.1 sequence-region NMRB01000001.1 1 1576180 species https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=416868 NMRB0100 ...
written 12 days ago by carina281710
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Comment: C: Which software is suitable for protein prediction from whole eukaryotic genomes?
... Hi, thank you for your answer. I am trying to understand how to get proteomes using gff files (I found this files for some of my species). I read a post where someone was asking how to do this (https://bioinformatics.stackexchange.com/questions/6865/can-a-gff-file-be-converted-to-a-fasta-file) and s ...
written 12 days ago by carina281710
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Which software is suitable for protein prediction from whole eukaryotic genomes?
... Hello, I want to try programms for Orthologous prediction (OrthoMCL for example), the programs work with proteomes but I have some genomes of eukaryotic organisms for which I don't have proteomic data, Could you please recomend me some software to predict protein sequences from whole genomes? ...
eukaryotic genome protein prediction written 15 days ago by carina281710 • updated 14 days ago by gb1.2k
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Answer: A: How to solve the different number of hits from tblastn when I use the option -pa
... It comes out the problem was not the "-parse_seqids" option, I discovered that every time I ran blast with some of the genomes I am using the results file had a different number of hits and this happens (with some genomes) in all blast versions after 2.3.0. I sent an e-mail to blast support and th ...
written 28 days ago by carina281710
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Problem with N sequences in fastqc file
... Hello, I am trying to filter a fastq file, I ran fastqc to get a quality report and I get an overrepresented sequence: sequence: NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN count: 39317 percentage: 0.13862182817994162 The fastq file has 28362777 sequences and the read length is 125. I use ...
fastq fastqc written 28 days ago by carina281710 • updated 27 days ago by yztxwd160
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How to get hit DNA sequences from psi-tBLASTn?
... Hello, I am running psi-tBLASTn and I wonder if there is any tool to get hit DNA sequences from psi-tBLASTn in order to perform the reciprocal BLASTx . I am using the following command to run psi-tblastn: tblastn -num_threads 20 -db blastdb_P_bachei -in_pssm A_thaliana_mMit_psiblast_10it.chk ...
psitblastn blast written 6 weeks ago by carina281710
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Comment: C: How to solve the different number of hits from tblastn when I use the option -pa
... I don't get any warning message ...
written 7 weeks ago by carina281710
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How to solve the different number of hits from tblastn when I use the option -parse_seqids in makeblastdb command?
... Hello, I am running tblastn and I am getting different hit numbers depending on if I add the option -parse_seqids to makeblastdb .I initially ran the following command to make the database: makeblastdb -in GCA_003024985.1_Erow_1.0_genomic_Euperipatoides_rowelli.fna -dbtype nucl then I ran tbl ...
makeblastdb tblastn blast written 7 weeks ago by carina281710

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Scholar 28 days ago, created an answer that has been accepted. For A: How to solve the different number of hits from tblastn when I use the option -pa

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