WikiSysop: Created page with "Answers to the Sequence logo exercise '''Written by:''' [http://www.dtu.dk/service/telefonbog/person?id=18103&cpid=214039&tab=2&qt=dtupublicationquery Rasmus Wernersson], April 2015 (latest update: April 2018) = Q1 = Image:Q1_logo.png * The "GT" consensus site is clearly seen (completely conserved: 2 bits of information), and it appears that there is also some signal on the exon side (preference for "G" on the position before) and on the intron side..."

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Created page with "Answers to the Sequence logo exercise '''Written by:''' [http://www.dtu.dk/service/telefonbog/person?id=18103&cpid=214039&tab=2&qt=dtupublicationquery Rasmus Wernersson], April 2015 (latest update: April 2018) = Q1 = Image:Q1_logo.png * The "GT" consensus site is clearly seen (completely conserved: 2 bits of information), and it appears that there is also some signal on the exon side (preference for "G" on the position before) and on the intron side..."

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Answers to the [[ExSeqLogos|Sequence logo exercise]]

'''Written by:''' [http://www.dtu.dk/service/telefonbog/person?id=18103&cpid=214039&tab=2&qt=dtupublicationquery Rasmus Wernersson], April 2015 (latest update: April 2018)

= Q1 =
[[Image:Q1_logo.png]]

* The "GT" consensus site is clearly seen (completely conserved: 2 bits of information), and it appears that there is also some signal on the exon side (preference for "G" on the position before) and on the intron side.
* The intron starts at position 11 - this means that position 1-10: EXON and 11-20: INTRON.

= Q2 - pretty LOGO=
[[Image:Q2_logo.png]]

= Q3 - frequency LOGO =
[[Image: Q3_logo.png]]

= Q4 - cross species comparison =
[[Image:Emblem-important_tiny.png‎]] '''IMPORTANT:''' This question is the easiest to answer, if you compare the DONOR and ACCEPTOR site separately across the 5 species (it's simply easier to spot the differences this way)

== Donor sites ==
[[Image:Q4_hs_donor.png]]
[[Image:Q4_dmel_donor.png]]
[[Image:Q4_Athal_donor.png]]
[[Image:Q4_scer_donor.png]]
[[Image:Q4_spombe.png]]

'''Observations:'''
* The animal (human + fruit fly) DONOR sites contain ~1 bit of information in the very last position of the exon (with a preference for "G"), and some information (< 1 bit) for the 4 positions following "GT" in the intron (=> in 6 intron positions in all)
* The plant (''Arabidopsis'') has the same pattern of some signal in the final 2 exon positions, but the signal in the intron is very weak after the "GT".
* The two fungal species show a pattern of next to no signal in the exon, but a '''very strong''' signal in the intron side beyond the GT.

== Acceptor sites ==
[[Image:Q4_hs_acceptor.png]]
[[Image:Q4_dmel_acceptor.png]]
[[Image:Q4_Athal_acceptor.png]]
[[Image:Q4_scer_acceptor.png]]
[[Image:Q4_spombe_acceptor.png]]

* Overall observation: the ACCEPTOR site motif is much more alike across all 5 species compared to the DONOR sites.
** In all cases there is next to no signal on the EXON side (after the "AG") - and there is a strong preference for T and C (~1 bit, as strong as it can get for a two-letter preference) immediately before AG.
** There is a diffuse preference for Ts in the region before AG in the animals + the plant.
** This preference for Ts is clearly centered around the -9 position in the fungi.

= Q5 - ''E. coli'' - Shine-Dalgano =
[[Image:Q5_ecoli_logo.png]]
* The START codon is mostly ATG, but GTG is common enough to be seen at the first position. If you zoom in at position 51-53 it is possible to a small number of other bases also being used in rare cases.
* A region with As and Gs can been seen a position 40-44 which could potentially be part of the SD sequence.

= Q6 SD zoom =
[[Image:Q6_ecoli_logo.png]]

The LOGO is consistent with the consensus sequence AGGAGG in the way, that it's not a huge disagreement with it. From the LOGO it appears that it's a bit of a stretch to claim A over G in any of the positions, but a clear overrepresentation of As OR Gs is clearly seen.

= Q7 - Kozak sequence (Yeast) =
[[Image:Q7_yeast_25-75.png|center]]
There appears to be a weak signal in the positions immediately before the START codon (especially the -3 position = coordinate 48).

[[Image:Q7_yeast_40-50_zoom1.png|center|Zoom of the 40-50 region]]
[[Image:Q7_yeast_40-50_zoom2.png|center|Zoom + Y axis rescale of the 40-50 region]]
<br style="clear: both" />

It can now clearly be seen that only position 48 (= 3 before the ATG) has information content above 0.2 bits.

[[Image:Q7_yeast_40-50_zoom_freq.png|center]]

By plotting a '''frequency plot''' of the same region, it can be seen that >50% of the sequences have A in position 48.

= Q8 - Signal peptides comparison =
[[Image:Q8_EUK.png|center]]
[[Image:Q8_gram_neg.png|center]]
[[Image:Q8_gram_pos.png|center]]

* '''Similarities:'''
** It's clearly seen that position -1 (just before the cleavage) and -3 is important and A (alanine) is preferred here (especially in the prokaryotes).
** In all three cases there is a stretch of '''hydrophobic''' (color = black) amino acids (L, V, A, I) in the middle of the signal peptide.
* '''Differences:'''
** The preference for A (alanine) at the -1 position is much stronger in the prokaryotic sequences
** The hydrophobic stretch is longer in Gram positive bacteria
** There is a preference for S/A at position -6 in Gram negatives that is not seen elsewhere
** There is no signal after the cleavage site in eukaryotes and some signal in the first few positions in both prokaryotic groups

= Q9 - seq2logo =
[[Image:Q9_EUK.png]]
* Yes - it clearly shows the same overall motif as above. Note that, unlike WebLogo, Seq2logo indicates positions with gaps by making the stack of letters more narrow.


= Q10 - small data sets =
[[Image:Emblem-important_tiny.png‎]] '''IMPORTANT:''' Compare the LOGOs from the small data set to the LOGO we got from the large data set (Question 9+10) and investigate if you can see the same pattern.

[[Image:Q11_pseudo_00.png]]
[[Image:Q11_pseudo_200.png]]

* The first plot (without pseudo-counts) is very noisy, and only the very overall trends can be seen: the tendency to have an "A" at the -1 position and a somewhat diffuse hydrophobic region.
* In the second plot (with the pseudo-counts) the picture looks a lot more like what we saw in the big data sets: a specific pattern at the -1 and -3 positions and the hydrophobic region much more in the shape with what we saw before.

ExSeqLogosAnswers - Revision history