User: Xylanaser

gravatar for Xylanaser
Xylanaser20
Reputation:
20
Status:
New User
Location:
Poland - Warsaw - SGGW/WULS
Last seen:
4 days, 10 hours ago
Joined:
3 years, 8 months ago
Email:
m***********@gmail.com

Posts by Xylanaser

<prev • 52 results • page 1 of 6 • next >
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Comment: C: HHpred installation problem
... latest pdb70 is here http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/ they update it (I do not have the latest one) , I can not find *.hmm file only pdb70_hhm.ffdata, pdb70_hhm.ffindex, pdb70_hhm_db, pdb70_hhm_db.index. I do not checked old releases: http://wwwuser.gwdg.de/~comp ...
written 11 days ago by Xylanaser20
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Comment: C: HHpred installation problem
... Hey. No :(. They did not answer me... If you learn something, I'm asking for help too. Cheers ...
written 12 days ago by Xylanaser20
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find bacteria lifestyle
... Hey. I have list of bacterias **example:** Gammaproteobacteria bacterium, Chloroflexi bacterium, marine metagenome, Anaerolineaceae bacterium, Erythrobacter sp., Sinorhizobium meliloti, Planctomycetes bacterium, Nonlabens ulvanivorans, Aequorivita sp., uncultured bacterium, Planctomycetaceae bacte ...
lifestyle bacteria taxonomy written 9 weeks ago by Xylanaser20
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Comment: C: Biopython coding, sublist from list dependently by id
... thanks ;) works fine! ...
written 10 weeks ago by Xylanaser20
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Biopython coding, sublist from list dependently by id
... Hey, I need help, I do not know how to deal with it: list_of_ids = [aasddaw23/2-20,aasddaw23/34-50,aasddaw23/67-100,fyyrr43/67-98,fyyrr43/80-120,poipoopop34/33-200,poipoopop34/144-222] #grouped list result = [[aasddaw23/2-20,aasddaw23/34-50,aasddaw23/67-100],[fyyrr43/67-98,fyyrr43/80-12 ...
python coding written 10 weeks ago by Xylanaser20 • updated 10 weeks ago by Eric Lim1.4k
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HHpred installation problem
... Hello. I am trying to install hhpred I have compiled HHsuite and add to .bashrc: export PATH="/home/xyl/hh-suite/build//bin:/home/xyl/hh-suite/build/scripts:$PATH" Everything works fine (I have downloaded scop70, pfam.32, uniclust30 and pdb70latest) Now i want to install hhpred , but im little c ...
hhpred protein written 11 weeks ago by Xylanaser20
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Biopython - multiple alignment issue - fliped parts of domain
... Hey. I have 'fliped domain' of protein family - alignment and i want to cut this multiple alignment in fasta on two part Nterm and Cterm and flip it to 'normal domain'. Can i do this in biopython? I never use this lib to MSA. Please advice me ! Best , X ...
python sequence protein biopython alignment written 5 months ago by Xylanaser20
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HH-Suite conda issue
... Hey biofreaks. I have a question to you about hh-suite installation under conda . Do you have the same issue with HHLIB path? - program can not find context_data.crf and cs219.lib. I solved this with `export HHLIB=/home/$USER/miniconda3/envs/bio3.7/share/hh-suite-3.0.0.beta3` because HHLIB in defa ...
hh-suite conda tool written 5 months ago by Xylanaser20 • updated 4 months ago by Biostar ♦♦ 20
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Comment: C: CUDASW++ query profile - someone know how to build it?
... I didn't recognize that i cant give profile inquery :(. Please close topic... ...
written 8 months ago by Xylanaser20
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CUDASW++ query profile - someone know how to build it?
... Hey anyone know how must look like query-profile for CUDASW++? [I found this https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-117][1] but not unerstand that. Is hmm profile will be well? Can u recognize this format of profile? [1]: https://bmcbioinformatics.biomedcentra ...
cudasw++ profile sequence protein written 8 months ago by Xylanaser20 • updated 7 months ago by Biostar ♦♦ 20

Latest awards to Xylanaser

Popular Question 5 months ago, created a question with more than 1,000 views. For Blast+ db problem
Popular Question 8 months ago, created a question with more than 1,000 views. For Blast+ db problem
Supporter 11 months ago, voted at least 25 times.
Popular Question 12 months ago, created a question with more than 1,000 views. For Blast+ db problem
Scholar 20 months ago, created an answer that has been accepted. For A: IHMP downloads - how?

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