Question: Hi,
I was wondering if anyone knew of a way to do a batch submission with HHpred? Currently I am able to paste each sequence individually and that can be pretty time consuming. If anyone has any tips or ideas how to submit the sequences as a batch I would appreciate any input.
Thank you

Aziza

Answer: I run hundreds of sequences using HHpred on the commandline. I have a few scripts for tabulating the output data if you're interested.

I don't know if commandline work is an option for you.

Ultimately a local install is always the best option.

EDIT:

To install, follow their instructions [here][1]. The tricky bit is making sure you set the environment variables correctly, but they provide all the instructions you should need.

Once you've done that, download the latest databases (note, they're *very* big and will take up a lot of space and take a long time to download).

`wget robots=off -r --no-parent -nH -nd -np -R *.html,*.txt -A .tgz http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/`

This will download **all** of their databases. If you just want, say, PDB, try:
`wget http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/pdb70_14Sep16.tgz`

Extract the database somewhere memorable

`tar xvzf pdb_70_14Sep16.tgz`

You're then ready to actually start searching, so you can do something like what's below. These options are specific to how I use the software though, so read their manual and determine what parameters for output you want.

for file in ./*.faa ; do
hhsearch -dbstrlen 50 -B 1 -b 1 -p 60 -Z 1 -E 1E-03 -nocons -nopred -nodssp -cpu 10 -i $file -d /path/to/database/pdb70_hhm.ffdata
done

You can replace this with a parallelisation call if you like using something like GNU parallels, but just be aware that you can run multiple sequences, but you can also specify that each sequence be searched against other HMMs with multiple cores, so don't over do it.

This will generate you a result file for each sequence that will look something like:

Query PAK_01787 PAK_01787 T4-like virus tail tube protein gp19 1997281:1997730 forward MW:16801
Match_columns 149
No_of_seqs 1 out of 1
Neff 1.0
Searched_HMMs 25094
Date Thu Dec 3 14:08:12 2015
Command hhsearch -cpu 10 -i /home/wms_joe/PVCs/PVC_operons/all/PAK_01787.fsa -d /home/wms_joe/Applications/HHSuite/databases/pdb70/pdb70_hhm.ffdata -B 10 -Z 10 -E 1E-03

No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1tvs_A Transactivator protein; 33.0 11 0.00046 25.9 0.0 14 27-42 38-51 (75)
2 3jqo_B TRAO protein; helical o 31.3 13 0.00051 25.6 0.0 32 44-77 41-72 (135)
3 2n01_B VIRB9 protein; T4SS, li 30.4 14 0.00054 24.1 0.0 25 42-66 32-60 (106)
4 1p65_A Nucleocapsid protein; v 20.6 27 0.0011 23.9 0.0 18 17-34 13-30 (73)
5 2wj5_A Heat shock protein beta 20.4 28 0.0011 20.3 0.0 31 80-113 13-43 (101)
6 2ltk_A Mono-cysteine glutaredo 18.4 32 0.0013 19.4 0.0 56 35-90 42-100 (110)
7 1lrw_B Methanol dehydrogenase 16.1 40 0.0016 23.5 0.0 33 109-141 12-46 (83)
8 1vyb_A ORF2 contains A reverse 15.6 42 0.0017 20.0 0.0 12 106-117 9-20 (238)
9 1kaf_A Transcription regulator 14.0 49 0.002 23.3 0.0 27 85-111 14-40 (108)
10 3but_A Uncharacterized protein 13.0 55 0.0022 21.4 0.0 39 88-126 2-40 (136)

No 1
>1tvs_A Transactivator protein; transcription regulation; NMR {Equine infectious anemia virus} SCOP: j.40.1.1 PDB: 1tvt_A
Probab=32.99 E-value=11 Score=25.86 Aligned_cols=14 Identities=43% Similarity=0.833 Sum_probs=12.3

Q PAK_01787 27 QMCFQSVSGLDISYDT 42 (149)
Q Consensus 27 qmcfqsvsgldisydt 42 (149)
|.||.. ||-|||..
T Consensus 38 qlCFlk--GLGIsYg~ 51 (75)
T 1tvs_A 38 QLCFLR--SLGIDYLD 51 (75)
T ss_pred HHHhcc--CCcccccC
Confidence 789999 99999973
...

At which point you can use/modify my script below, which will turn the output file in to a tab delimited file (I then concatenate all my results together so they can be viewed in spreadsheets etc. The script as it is will only return the *best hit* (No 1) so if you want more than that you'll have to get creative!

https://gist.github.com/jrjhealey/d2c9232bd7fc70d16f8939d6a6f58f88
[1]: https://github.com/soedinglab/hh-suite