RNAhub (U6)

U6-0c44b443 (U6)

The raw output files for each step of the pipeline can be found here.

Input: sequence:

>u6 human
GUGCUCGCUUCGGCAGCACAUAUACUAAAAUUGGAACGAUACAGAGAAGAUUAGCAUGGCCCCUGCGCAAGGAUGACACG
CAAAUUCGUGAAGCGUUCCAUAUUUUU

Database: metazoa

Rfam scan:

 rank     E-value  score  bias  modelname  start    end   mdl trunc   gc  description
  (1) !   6.3e-29  109.4   0.0  U6             1    107 +  cm    no 0.46  U6 spliceosomal RNA

Rfam accession for U6: RF00026
saved to /home/rnahub/rnahub-web/media/jobs//U6-0c44b443/seq+RF00026_seed.fa
>u6 human
GUGCUCGCUUCGGCAGCACAUAUACUAAAAUUGGAACGAUACAGAGAAGAUUAGCAUGGCCCCUGCGCAAGGAUGACACG
CAAAUUCGUGAAGCGUUCCAUAUUUUU
>AB010698.1/46416-46518
GUCCCUUCGGGGACAUCUGAUAAAAUUGGAACGAUACAGAGAAGAUUAGCAUGGCCCCUG
CGCAAGGAUGACACGCAUAAAUCGAGAAAUGGUCCAAAUUUUU
>AARH01001853.1/272694-272592
GUCUCUUCGGAGACAUCUGAUAAAAUUGGAACGAUACAGAGAAGAUUAGCAUGGCCCCUG
CGCAAGGAUGACACGCACAAAUCGAGAAAUGGUCCAAAUUUUU
>X60506.1/390-492
GUCCCUUCGGGGACAUCCGAUAAAAUUGGAACGAUACAGAGAAGAUUAGCAUGGCCCCUG
CGCAAGGAUGACACGCACAAAUCGAGAAAUGGUCCAAAUUUUU
>AC146705.11/15272-15374
GUCCCUUCGGGGACAUCCGAUAAAAUUGGAACGAUACAGAGAAGAUUAGCAUGGCCCCUG
CGCAAGGAUGACACGCACAAAUCGAGAAAUGGUCCAAAUUUUU
[...]
cmalign RF00026.cm /home/rnahub/rnahub-web/media/jobs//U6-0c44b443/seq+RF00026_seed.fa > /home/rnahub/rnahub-web/media/jobs//U6-0c44b443/seq+RF00026_seed.sto
/home/rnahub/opt/hmmer/hmmer-3.3.2/bin//esl-alistat /home/rnahub/rnahub-web/media/jobs//U6-0c44b443/seq+RF00026_seed.sto > /home/rnahub/rnahub-web/media/jobs//U6-0c44b443/rfam_stats.txt
cmd: /home/rnahub/opt/hmmer/hmmer-3.3.2/bin//esl-alistat /home/rnahub/rnahub-web/media/jobs//U6-0c44b443/seq+RF00026_seed.sto > /home/rnahub/rnahub-web/media/jobs//U6-0c44b443/rfam_stats.txt
Rscape DONE

Query u6 length 107 in the alignment seq+RF00026_seed.sto number of columns with low coverage (<50%) for the query sequence 1; coverge for the query: 99%

R-scape on rfam alignment:

The secondary structure proposed contains 19 base pairs with 3 base pairs observed to covary.

The final alignment (*cacofold.sto) can be found here.

BPAIRS 19
avg substitutions per BP  23.2
BPAIRS expected to covary 10.1 +/- 1.9
BPAIRS observed to covary 3

List of covarying basepairs (#3)

In given structure	Left Position	Right Position	Score	E-value	p-value	Substitutions	Power
*	2	50	272.77949	4.86652e-07	8.42249e-11	49	0.86
*	3	49	258.80373	1.66548e-06	2.88245e-10	59	0.89
*	5	45	214.78797	8.08633e-05	1.3995e-08	56	0.88

* Base pair in the structure
~ Both residues unpaired in the structure, or no structure is present
' ' At least one residue is involved in other pairing in the structure

Alignment statistics:

Alignment number:    1
Format:              Stockholm
Number of sequences: 189
Alignment length:    225
Total # residues:    20223
Smallest:            85
Largest:             167
Average length:      107.0
Average identity:    70%

R-scape on nhmmer alignment:

Search:

There is no statistically significant covariation in the final alignment

The secondary structure proposed contains 26 base pairs with 0 base pairs observed to covary.

avg substitutions per BP  5.7
BPAIRS expected to covary 3.8 +/- 1.4
BPAIRS observed to covary 0

The final nhmmer alignment can be found here.

Alignments from each iteration: iteration 1, iteration 2, iteration 3.

Alignment statistics:

Alignment number:    1
Alignment name:      u6
Format:              Stockholm
Number of sequences: 178
Alignment length:    1238
Total # residues:    18148
Smallest:            62
Largest:             106
Average length:      102.0
Average identity:    94%

Job log: