User: Xylanaser

gravatar for Xylanaser
Xylanaser60
Reputation:
60
Status:
Trusted
Location:
Poland - Warsaw - SGGW/WULS
Last seen:
3 weeks, 3 days ago
Joined:
4 years, 11 months ago
Email:
m***********@gmail.com

Posts by Xylanaser

<prev • 61 results • page 1 of 7 • next >
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how to get secondary structure from DSSP?
... Hey. Is there quick way (biopython or something) to retrive secondary structure from dssp file? eg 'HHHHHHHHHHEEEEEEEEEEEECCCCCCCCHHHHHHEEEEEEEEE' I need to get SS by pdb id and build FASTA like records >3gja HHHHHHHHHHEEEEEEEEEEEECCCCCCCCHHHHHHEEEEEEEEE >3akl CCCCCCCCCCCCEE ...
pdb protein structure dssp written 7 months ago by Xylanaser60 • updated 7 months ago by Mensur Dlakic6.9k
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Comment: C: ECOD HHMdb to hh-suite
... Thank you for answer :) ...
written 7 months ago by Xylanaser60
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ECOD HHMdb to hh-suite
... Hello, do you know how I am suppose to make HH-suite database from ecod.latest.F99.hhm_db from: http://prodata.swmed.edu/ecod/complete/distribution hhsuite databases have many other files: a3m.ffdata, a3m.ffindex etc. do you know how to solve this? Best, X edit: I found this now: https://gi ...
hh-suite hhpred hhm written 7 months ago by Xylanaser60 • updated 7 months ago by Mensur Dlakic6.9k
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Answer: A: Download pnly latest sequences from GenBank
... https://www.ncbi.nlm.nih.gov/books/NBK279680/ update_blastdb.pl check last paragraph ;) best wishes ...
written 10 months ago by Xylanaser60
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Comment: C: secondary structure comparison - how to approach this? / tools?
... Thank you, it solves my problem. Best wishes ...
written 10 months ago by Xylanaser60
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secondary structure comparison - how to approach this? / tools?
... I want to compare two secondary structures of aligned proteins. I do not know exactly how to do it well. Example: EEEEEEEEEEETTTTTTHCTTTEEECTTTEEECTTECTCCCHHHHHHHHHCHCCTHHEEEETTTEEECTTTEEECTTTEEC EEEHHHHHHHTTTTTTTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEECCCCCCCCCCEEEEEEEEEEEEEE Exampl ...
python secondarystructure protein structure written 10 months ago by Xylanaser60 • updated 10 months ago by Mensur Dlakic6.9k
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Comment: C: HMP proteomic fasta size? HMP statistics?
... I saw that. It must be error. On HMP1v2 (2014) site project (https://hmpdacc.org/hmp/HMRGD/) archive with protein fasta weight 1,2gb (~2gb unziped). I remeber that HMP sequencing protein fasta translations too ( ͡° ʖ̯ ͡°) ...
written 10 months ago by Xylanaser60
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HMP proteomic fasta size? HMP statistics?
... Hey do you know where can i find HMP statistics? https://www.hmpdacc.org/catalog/statistics.php  those not work I know that HMP have sites and about 2000 reference genomes, but where can i find info about number of metagenomes ? I found this: https://www.ncbi.nlm.nih.gov/bioproject/28331 And ncbi f ...
fasta hmp protein written 10 months ago by Xylanaser60
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standalone CDsearch version?
... Hey is it somewhere a CDsearch standalone version? Or i need simulate it somehow with BLAST? Can u give me advice? cheers ...
cdsearch sequence cdd bioinformatics written 14 months ago by Xylanaser60 • updated 14 months ago by h.mon31k
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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 15 months ago by Xylanaser60

Latest awards to Xylanaser

Popular Question 7 months ago, created a question with more than 1,000 views. For blaSTorage intallation problem
Popular Question 7 months ago, created a question with more than 1,000 views. For Blast+ db problem
Popular Question 7 months ago, created a question with more than 1,000 views. For How can I get FASTA if i have Names of proteins ?
Popular Question 10 months ago, created a question with more than 1,000 views. For blaSTorage intallation problem
Popular Question 10 months ago, created a question with more than 1,000 views. For Blast+ db problem
Popular Question 10 months ago, created a question with more than 1,000 views. For How can I get FASTA if i have Names of proteins ?
Scholar 10 months ago, created an answer that has been accepted. For A: IHMP downloads - how?
Popular Question 13 months ago, created a question with more than 1,000 views. For blaSTorage intallation problem
Popular Question 20 months ago, created a question with more than 1,000 views. For Blast+ db problem
Popular Question 23 months ago, created a question with more than 1,000 views. For Blast+ db problem
Supporter 2.2 years ago, voted at least 25 times.
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Blast+ db problem
Scholar 2.9 years ago, created an answer that has been accepted. For A: IHMP downloads - how?

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