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Question: Why is there a difference in results when using HHpred server and HHsearch standalone
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When I use the server HHpred and search against PDB70 I get different results when I run it locally (run HHblits, add ss then HHsearch). I use the same setting as the server (I copy these from the raw output tab on the results from the server). I do, however, get the same results when I search against pfam. Can anyone help?

HHpred Server Results

Query sp|Q5BJD5|TM41B_HUMAN Transmembrane protein 41B OS=Homo sapiens OX=9606

GN=TMEM41B PE=1 SV=1

Match_columns 291

No_of_seqs 260 out of 1755

Neff 8.62981

Searched_HMMs 46150

Date Thu Nov 1 17:25:23 2018

Command hhsearch -cpu 8 -i ../results/full.a3m -d /cluster/toolkit/production/databases/hh-suite/mmcif70/pdb70 -o ../results/1206399.hhr -oa3m ../results/1206399.a3m -p 20 -Z 250 -loc -z 1 -b 1 -B 250 -ssm 2 -sc 1 -seq 1 -dbstrlen 10000 -norealign -maxres 32000 -contxt /cluster/toolkit/production/bioprogs/tools/hh-suite-build/data/context_data.crf

No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM

1 3D31_D Sulfate/molybdate ABC t 91.3 7.9 0.00017 33.9 19.9 272 9-291 1-294 (295)

2 3B5X_B Lipid A export ATP-bind 66.9 1.5E+02 0.0032 28.5 14.3 188 89-291 7-194 (582)

3 2ONK_C membrane protein; membr 60.4 1.4E+02 0.003 25.8 17.8 264 25-291 1-282 (284)

4 6BPL_A Lipid A export ATP-bind 59.8 2E+02 0.0044 27.6 13.3 188 89-291 7-194 (582)

5 2KS1_A Receptor tyrosine-prote 53.8 47 0.001 19.4 4.2 27 265-291 18-44 (44)

HHsearch local results

Query sp|Q5BJD5|TM41B_HUMAN Transmembrane protein 41B OS=Homo sapiens OX=9606

GN=TMEM41B PE=1 SV=1

Match_columns 291

No_of_seqs 256 out of 1602

Neff 6.9

Searched_HMMs 60862

Date Tue Nov 20 10:57:43 2018

Command hhsearch -i /home/shah/seq/tests/test_addss/tmem41b_human_w_ss.a3m -d /home/shah/db/pdb70/pdb70_hhm.ffdata -o /home/shah/seq/tests/test_addss/tmem41b_ss_test4.hhr -p 20 -Z 250 -loc -z 1 -b 1 -B 250 -ssm 2 -sc 1 -seq 1 -dbstrlen 10000 -norealign -maxres 32000 -contxt /home/shah/hh/hh-suite-3.0-beta.3/data/context_data.lib

No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM

1 6B87_C TMHC2_E; De novo design 63.5 84 0.0014 24.6 8.4 74 53-126 15-89 (111)

2 6B87_D TMHC2_E; De novo design 61.8 84 0.0014 24.6 7.4 74 53-126 15-89 (111)

3 4HUQ_S Energy-coupling factor 53.4 62 0.001 27.5 6.3 65 98-162 1-72 (174)

4 3RLB_A Putative uncharacterize 31.1 2E+02 0.0032 25.0 6.1 70 83-161 2-79 (192)

5 4Z7F_E Folate ECF transporter; 24.4 2E+02 0.0032 25.4 4.9 64 99-162 19-90 (199)

ADD COMMENTlink 14 months ago shahram.mesdaghi • 0
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The difference in "Searched_HMMs" means that the searches are performed against different (versions of) databases, i think.

BTW, hhpred uses hhblits to construct input a3m before the final search. Did you surely turn it off with the "Parameters" tab?

ADD REPLYlink 16 months ago
fishgolden
• 390
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Thanks for that! I managed to obtain the same database that the server is using and still I get different results.

Both my server and local run uses HHblits to generate the a3m files.

I have realised, however, that I am using HHsuite 2.16 (apt get version) and the server is using 3.0. I'm going to update and see if that makes any difference.

Thanks you for your time!

ADD COMMENTlink 14 months ago shahram.mesdaghi • 0

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