mfold command line vs mfold web

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eandres
Posts: 3
Joined: Fri Dec 09, 2022 1:07 pm

mfold command line vs mfold web

Post by eandres »

Dear all,
I need to run mfold in hundred/thousands of fasta sequences, so I'd like to use the command line version.
I've used one of the sequences in the web site and I've obtained 12 structures (all parameter by default). However when using the mfold command line with the same fasta file I obtained 0 structures:

mfold version 3.6
REUSE= NO
kk.pnt created.
Sequence length is 387
Folding at 37 degrees using version 3.0 dat files.
Save file created using nafold.
Save file is empty. No foldings.
Job Aborted

So not sure what is happening .. should I take something into account ? Did I miss anything ?

Thanks in advance
zukerm
Posts: 2
Joined: Tue Jul 12, 2022 3:54 am

Re: mfold command line vs mfold web

Post by zukerm »

From the error message that you received,

Save file is empty. No foldings.
Job Aborted

I conclude that the mfold software is not installed properly.

You need to give me information. I assume that you downloaded the mfold software from http://www.unafold.org/mfold/software/d ... -mfold.php Is that correct. What platform are you running it on? What is in the log file?

In any case, you are using the software incorrectly if you want to fold many sequences at the same time. You need to use the underlying folding program, 'nafold'. This is run interactively. When you run the command: 'nafold', enter '0' at the first prompt for a 'regular run'. For 'run mode', enter '2' for 'Multiple Molecules'. Then enter the sequence file name (FASTA format). Then enter information as it is requested. Allow the default energy rules to be used. If that fails, then you don't have a proper installation. Select Y for 'printer output'. I strongly suggest entering a file name. Enter N (No) for the other two kinds of output, and finally enter '10' for 'begin folding'

For the input file 'rand.seq' below:
>r1
CAGCACGCCGACCAUCGCGUGAGAGAUUCCACUAGGGAUACGAAUCAUUGCCUUGUCGCC;
>r2
CCAACGUGCGGGCAUUGUGACUGCGGUCGUCUCAUAGUGACACGGCAACUGGCGCGCGUU;
>r3
AGGCAAUACUAUCGUCCUAAUCGGGCGGGCAGCCGAAAAAGAUUUCCUUCGAGGCCGGUU;
>r4
GCGAUGGGUCGGCCUCAGAUCGGAUACUUUCUAGGACCGGAAGUCUAGAAGAUUCCUCAU;
>r5
CCGGUCUCAACAAUUACUAUCAAAUUAUGGGAGCCAGCUACUCGGCUGUAAUCGACAUAG;
>r6
CAUCAGCUUAUCGCUAACUUUAACAGUGUCGUUCUCCCUACGAUCAGCGACGACGUCACG;
>r7
UUCUACUGAGCGAACCGCUGCGAAAAUUCCGAAAUAAAUACGUCGGCAGAAUCAAAGAGG;
>r8
CGUUCUGCAUUCACACUUGUUUGGUCGCAAUAUUGAACACACUCUAUUGGGUAUACUUCC;
>r9
AUAUCGAUAACGGACCCUACAAGGUGCUAUACGAUCUACGAUCAAGGGGUAUGGCACCUA;
>ra
GUUCGAGCAAGGGCCUUCUUCUCAACAAUUUCUGAGCGGAUUGCGGAUGGACGGCCCAUC;
>rb
CCCAACUGCCGUACGAACUGAAGACCCGGGGGUAGGGACCCACACCCCCUUAAUCAGGAG;
>rc
GGUGGGAAUUGGUUCCGAAGGAGGCUCAUUCGCUGUUGAAAGGAUGGUUAUACGUCAACG;
>rd
AUCGUAGGGAGAGCGAGGACCUCACCAAGGGACCAAUCCUGGUUAACGGCAAGAUAGCGC;
>re
GUGUUUACAAGAGGGUGAACGUGCGUGCCCAGUCAGCUGGAGACGGAACAAGGGACUUAG;
>rf
GCGACUGCAAUCGUUCGCCGGGUACCAAUAUCAUGCUAAUUAUAUCUAGGGCACUUUGGG;
>rg
AUUGGUAAGCGCUCGUUUUUUACACCCUACGUUUGCUUGAGUGAAUGCAAAUGAGGCCUG;
>rh
GGGAGCCCAUGGCGCCUUCAAGUAACCUACUAAACGCAAUGAAGGGAUUGUUUGCUGUCG;
>ri
AGGUUAAAGCUGUCUCGGGAGGACGCUAUUGCAGGACAACUGAAUCAUUUAUCUAACUCC;
>rj
UUCGCUAAAUUGAUUCCGAGGGAGAAAUUAUAGCCCGGCCGGGCUGUCGUCUAGCGUGCA;
>rk
CUGGUAAUCAAAGACAAUUUCCAUUCAACUGCGUAUGUCCGCGGGUUCGCGACACAUAGC;

the result is

Sequence 1 Structure 1

Folding bases 1 to 61 of r1
dG = -12.50

10 20 30
CAGCACGC CATC - GAG--| A
CGAC GC GTGA ATTCC C
GCTG CG TACT TAGGG T
;CC----- TTC- T AAGCA^ A
60 50 40



Sequence 2 Structure 1

Folding bases 1 to 61 of r2
dG = -20.70

10
CC .-G| TTG
AACGTGCG GCA \
TTGCGCGC CGT T
;- \ -^ CAG
60 20


30
G----- C AT
GTCGT TC \
CGGCA AG A
GGTCAA C TG
50 40



Sequence 3 Structure 1

Folding bases 1 to 61 of r3
dG = -14.40

10
A---- .-AATACTA| TA
GGC TCGTCC \
CCG GGCGGG A
;TTGG \ -------^ CT
60


30 40
GCAGC AAAG
CGAA A
GCTT T
GA--- CCTT
50



Sequence 4 Structure 1

Folding bases 1 to 61 of r4
dG = -12.60

10 20
GC--------------| GGG - C TCGG
GAT TCGG CCT AGA A
CTG GGCC GGA TCT T
;TACTCCTTAGAAGAT^ AA- A - TTCA
60 50 40 30



Sequence 5 Structure 1

Folding bases 1 to 61 of r5
dG = -9.10

10 20
CCG-- .-TCAACAATTA| CA
GTC CTAT A
CAG GGTA A
;GATA \ ----------^ TT
60 30


40
GAGC- A
CAGCT C
GTCGG T
CTAAT C
50



Sequence 6 Structure 1

Folding bases 1 to 61 of r6
dG = -11.80


.-CATC| TT
AGC \
TCG A
\ ----^ CT



20 30 40
AACTTTAACA T C C AC
GTG CGTT TC CT G
CAC GCAG AG GA A
;G-------- T C C CT
60 50



Sequence 7 Structure 1

Folding bases 1 to 61 of r7
dG = -7.20

10
-- .-ACTG| A
TTCT AGCG \
GAGA TCGC A
;G \ ----^ C
60


20 30
GC AAATT AATA
GA CCGA A
CT GGCT A
AA AAGAC GCAT
50 40



Sequence 8 Structure 1

Folding bases 1 to 61 of r8
dG = -8.10

10
.-C -----| AT CAC
GTTC TGC TCA T
CAAG ACG GGT T
\ - TTATA^ CT TTG
30 20


40 50
ACACTCTATT TA
GGG T
CCT A
;--------- TC
60



Sequence 9 Structure 1

Folding bases 1 to 61 of r9
dG = -17.90


.-ATA| A
TCG T
GGC A
\ ---^ A
10


20 30 40
ACCCTACA GA ACG
AGGTGCTATAC TCT \
TCCACGGTATG GGA A
;A------ G- ACT
60 50



Sequence 10 Structure 1

Folding bases 1 to 61 of ra
dG = -19.10

10 20 30
GTTCGAGCAA| T TC AA CT
GGGCC TCT TC CAATTT G
CCCGG AGG AG GTTAGG A
;CTA------^ C T- GC CG
60 50 40



Sequence 11 Structure 1

Folding bases 1 to 61 of rb
dG = -14.20

10 20 30
CCCAACTGCCGTACGAA| AGACCC A- G
CTGA GGGGGT GG \
GACT CCCCCA CC A
;GAG-------------^ AATT-- CA C
60 50 40



Sequence 12 Structure 1

Folding bases 1 to 61 of rc
dG = -11.30

10
TG - T -| G
--GG G GAAT GG TTCC \
TT C CTTA TC GAGG A
\ GT G C G^ A
30 20


40
GAAAG GT
GATG T
CTGC A
;GCAA AT
60 50



Sequence 13 Structure 1

Folding bases 1 to 61 of rd
dG = -10.70


.-A| AGG
TCGT \
AGCG G
\ -^ AGA
10


20 30
.-GGACCTC A AC
ACCA GGG \
TGGT CCT C
\ ------- - AA
40


50
TAACG AA
GC G
CG A
;CG-- AT
60



Sequence 14 Structure 1

Folding bases 1 to 61 of re
dG = -15.50

10
.-G| AA
TGTTTAC G
GCAAGTG A
\ -^ GG
20


30 40
TGC-- G AGTCAG G
GT CCC CTG A
CA GGG GGC G
;GATT - AACAA- A
60 50



Sequence 15 Structure 1

Folding bases 1 to 61 of rf
dG = -8.80


| C C
--GCGA TG A
CGCT GC A
\ ^ T T
10


20 30 40
CGGGTA TATCA AATTA
CCAA TGCT T
GGTT ACGG A
;G---- TC--- GATCT
60 50



Sequence 16 Structure 1

Folding bases 1 to 61 of rg
dG = -11.10

10
.-ATTG ---| G
GTAA GC C
CATT TG T
\ ---- TTT^ C
20


30 40
AC--- A TTGA
CCT CGTTTGC G
GGA GTAAACG T
;GTCC - TAAG
60 50



Sequence 17 Structure 1

Folding bases 1 to 61 of rh
dG = -12.50

10 20
-- G CC TG CG --------| A
GG AGC A G CCTTCA AGTA \
CT TCG T T GGAAGT TCAT C
;G G TT GT AG AACGCAAA^ C
60 50 40 30



Sequence 18 Structure 1

Folding bases 1 to 61 of ri
dG = -11.00

10
A-- .-A| T T G
GGTTA AGC GTC C G
TCAAT TCG CAG G G
;CC \ -^ - - A
60 20


30
ATTG------- GA
CAG \
GTC C
CTATTTACTAA AA
50 40



Sequence 19 Structure 1

Folding bases 1 to 61 of rj
dG = -17.60

10
TT--- .-AATTGA| G
CGCTA TTCC \
GCGAT GAGG A
;ACGT \ ------^ G
60 20


30
AAATT G
ATAGCCC G
TGTCGGG C
CTGC- C
50 40



Sequence 20 Structure 1

Folding bases 1 to 61 of rk
dG = -10.30

10
.-C| T CAA
TGG AAT A
ACC TTA G
\ -^ T ACA
20


30 40
TTCAACT G C- G
GC TATGT CGCG G
CG ATACA GCGC T
;------ - CA T
60 50


I strongly suggest that you read the manual at: http://www.unafold.org/doc/mfold-manual/ (you can download a pdf version).

What sort of output are you looking for?

It would be much easier for you to install the UNAFold software.
eandres
Posts: 3
Joined: Fri Dec 09, 2022 1:07 pm

Re: mfold command line vs mfold web

Post by eandres »

Dear Zukerm !

Thanks for your help !! We have managed to run nafold and check the error. Now mfold is working and the results from the webserver and the command line are 100% identical !

Merry Christmas
Aptamer
Posts: 1
Joined: Wed Aug 02, 2023 4:06 am

Re: mfold command line vs mfold web

Post by Aptamer »

Dear scholar, I have encountered the same problem, may I ask how you finally solve this problem?
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