User: Kay

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Kay0
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Posts by Kay

<prev • 11 results • page 1 of 2 • next >
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how to do a MK test analysis
... Hi everyone, I'm trying to use [MK test version 2.0][1] But I don't quite understand the data input structure. It's asking for Dn and Ds (Integer-valued counts of between-species divergence for non-synonymous and synonymous substitutions), I understand yn00 from PAML might help with that, Pn and Ps ...
mk test mcdonald-kreitman test paml written 3 months ago by Kay0
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Answer: A: Genome structural annotation (augustus)
... have you thought of passing gff file and reads into Maker and training with SNAP ...
written 4 months ago by Kay0
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Comment: C: how to change the sequence ID and order of sequences in a file to match an align
... thanks, figured another way to do it using a script. ...
written 4 months ago by Kay0
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Comment: C: how to change the sequence ID and order of sequences in a file to match an align
... Assuming alignment file is also in fasta file, and the sequence ID is not truncated. Is it possible to sort my nucleotides then to have something like: >augustus_masked-scf7180006947290-processed-gene-0.5-mRNA-1 ATGAGTGAAATACGGAGTTTAAACATTTTCGATGCCAACAGCCAGAACTCATCAGAATTT AGACGTAATAT ...
written 4 months ago by Kay0
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(Closed) how to sort protein and nucleotide sequences based on IDs
... I have a protein alignment file in fasta format and nucleotide sequences of the original proteins. How can I sort my nucleotide sequences such that their IDs match that of the alignment file, Assuming my protein sequences looks like: >Seq1 MYHLGQGDPEPDIN >Seq2 MYGGQGDPEPYIN ...
fasta written 4 months ago by Kay0
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Comment: C: how to change the sequence ID and order of sequences in a file to match an align
... using this approach I will have to extract the new sequence ID from the alignment file and write it to a new file: augustus_masked-scf7180006947290 DILT_0000424901-mRNA-1 maker-scaffold10x_338_pilon-snap MS3_04642.1 and then use `csvtk sort`, what if I have ma ...
written 4 months ago by Kay0
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Comment: C: how to change the sequence ID and order of sequences in a file to match an align
... thanks for your reply, but would for few sequences, I'm talking of when I have like 50 sequences (or more). Also, Im not sure if truncating the sequence ID truncated to 32 characters makes Identifying unique, it appears it just truncates them, meaning in case of sequences where sequences have simil ...
written 4 months ago by Kay0
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how to change the sequence ID and order of sequences in a file to match an alignment output file
... Hi, I have two files, one is protein sequences of a group of genes, and the other is their corresponding nucleotide sequences. >maker-scaffold10x_338_pilon-snap-gene-0.71-mRNA-1 MHLKNGDPKPTIKPNQCTLFGFRFCPYVDRVRMVLQYYNVPHDNVWIHLYSKPDWYLELY PVGKVPLLITKEGKTIVESDAIIRYLDETIGNKSLMSLCGEAEF ...
python script written 4 months ago by Kay0 • updated 4 months ago by shenwei3564.6k
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Comment: C: ete3 evol doesnt work on test data
... thanks, seems to work on the test data, and paml test data now, I installed ete toolkit from github in a new conda environment although my data returns a few errors (might gahe to do with my data) ...
written 6 months ago by Kay0
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ete3 evol doesnt work on test data
... Hi, I recently installed [ete][1] via conda, so have a new environment for ete. I was able to use it to generate trees using ete3 build -w standard_raxml -a NUP62.aa.fa -o output_tree but when I try to run: ete3 evol -t ECP_EDN_15.nw --alg ECP_EDN_15.fasta -o results1/ --models fb M2 SLR ...
ete3 paml ete written 6 months ago by Kay0 • updated 6 months ago by WouterDeCoster39k

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