User: mbrav005

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mbrav0050
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Posts by mbrav005

<prev • 13 results • page 1 of 2 • next >
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Structure superiposition Alignment viewer
... Hello all. I currently have 3 structures superimposed onto each other in pymol and would like to see the sequence alignment of this superposition. Is this possible and if so how? I aligned the structures by using the cealign command. Ideally I would like to be able to scroll over parts of the alignm ...
protein alignment pymol structure written 5 weeks ago by mbrav0050 • updated 4 weeks ago by jgreener250
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Comment: C: Swiss-model model quality
... I was suspecting that it is due to the pdb lacking the full length of the alignment, I will try to adress this issue within interactive mode. Actually I have been just trying to see how swiss-model scores and models my seqeunce of 100% identity. It makes more sense in the future to just use the raw ...
written 6 weeks ago by mbrav0050
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Swiss-model model quality
... Hey all, I have been trying to model my sequences via swiss-model and I believe if im not mistaken a good/ok model is determined by a higher QMEAN>-4.0. I am wondering how a structure can get such a low QMEAN i.e. -7.0 if the sequence identity between the template and target are 100%? For exampl ...
swiss-model alignment structure written 6 weeks ago by mbrav0050 • updated 6 weeks ago by Mensur Dlakic6.6k
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Comment: C: Taxidlist output question (BLAST+)
... Ok, thats also what I was thinking along the lines of, thank you ...
written 9 weeks ago by mbrav0050
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Taxidlist output question (BLAST+)
... hello all, I am wondering how when I use a Taxidlist of only 169 unique taxids in my blastp search, When I use this taxidlist in my next blastp search, i get 177 uniq taxids in the output blast search? How am I gaining 8 new unique taxids when I only started with 169? Shouldn't I only get less or at ...
blast written 9 weeks ago by mbrav0050
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Obtaining FASTA format from blastp output
... Is it possible to convert BLAST hits from the blastp command in order to have the output into a FASTA file containing the sequences of the hits from the blast search? I do not want any statistics or alignments, just the hits in FASTA format. Alternatively, if this is not possible, is there a way to ...
fasta blast written 9 weeks ago by mbrav0050
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Comment: C: *BLAST Database error: DB contains no accession info
... marcob@DESKTOP-E3I33R3 ~/Phylogenetic_research/RpsB $ export BLASTDB_LMDB_MAP_SIZE=1000000 marcob@DESKTOP-E3I33R3 ~/Phylogenetic_research/RpsB $ makeblastdb -in RpsB_nr_1k.faa -parse_seqids -dbtype prot Building a new DB, current time: 07/09/2020 15:53:24 N ...
written 10 weeks ago by mbrav0050
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Comment: C: *BLAST Database error: DB contains no accession info
... Here are the headers $ sudo grep "^>" RpsB_nr_1k.faa | head -3 >EFF0795401.1 30S ribosomal protein S2 [Escherichia albertii] >AAV39589.1 ribosomal protein S [synthetic construct] >AHA63052.1 SSU ribosomal protein S2P [Shigella dysenteriae 1617] also, how would I go abou ...
written 10 weeks ago by mbrav0050
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Comment: C: *BLAST Database error: DB contains no accession info
... when I add -parse_seqids it says $ makeblastdb -in RpsB_nr_1k.faa -dbtype prot -parse_seqids Building a new DB, current time: 07/09/2020 14:29:29 New DB name: /home/marcob/Phylogenetic_research/RpsB/RpsB_nr_1k.faa New DB title: RpsB_nr_1k.faa Sequence type: Protein ...
written 10 weeks ago by mbrav0050
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*BLAST Database error: DB contains no accession info
... When I run my blastp search against the NCBI swissprot it works fine. Here is my output $ sudo blastp -db swissprot -query RpsB.faa -outfmt "7 std taxid" -seqidlist SACC_960_hits_SI2vs5kRpob.pacc.bsl # BLASTP 2.10.1+ # Query: sp|P0A7V0|RS2_ECOLI 30S ribosomal protein S2 OS=Escheric ...
software error written 10 weeks ago by mbrav0050

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