Answers.Body: <p>I found the following two files in <a href="https://downloads.yeastgenome.org/sequence/S288C_reference/" rel="noreferrer">https://downloads.yeastgenome.org/sequence/S288C_reference/</a>:</p>
  
  <ul>
  <li><a href="https://downloads.yeastgenome.org/sequence/S288C_reference/SGD_all_ORFs_3prime_UTRs.fsa" rel="noreferrer">SGD_all_ORFs_3prime_UTRs.fsa</a></li>
  <li><a href="https://downloads.yeastgenome.org/sequence/S288C_reference/SGD_all_ORFs_5prime_UTRs.fsa" rel="noreferrer">SGD_all_ORFs_5prime_UTRs.fsa</a></li>
  </ul>
  
  <p>According to the README files in the same directory, these are (the README for the 5' file is equivalent):</p>
  
  <blockquote>
    <p>SGD_all_ORFs_3prime_UTRs.README</p>
    
    <p>Information about the SGD_all_ORFs_3prime_UTRs.fsa file.</p>
    
    <p>This file contains sequences for predicted 3' UTR sequences for all
    characterized, uncharacterized and dubious ORFs in S288c.</p>
    
    <p>3' UTR coordinates were retrieved from YeastMine
    (yeastmine.yeastgenome.org) on July 3, 2017 using the stop coordinates
    of both the predicted transcript and gene sequences. A BED file with
    these coordinates was made. BED files were fixed on Sept 22, 2017 to
    account for strandedness. Sequences were batch downloaded again in
    FASTA format from USCS Genome Table Browser on Sept 22, 2017
    (<a href="https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=604915183_aUc9FZ1vwyAccGti1uI0wteYEM7x" rel="noreferrer">https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=604915183_aUc9FZ1vwyAccGti1uI0wteYEM7x</a>)</p>
    
    <p>File created: 2017-08-25</p>
  </blockquote>
  
  <p>Those therefore seem to be the 3' and 5' UTR sequences of all yeast genes in FASTA format and should be exactly what you need. </p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-05-12T00:16:53.643Z
Answers.Text: The link is broken
Answers.UserDisplayName: Pengyao
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-05-12T12:25:04.713Z
Answers.Text: @Pengyao yes, apparently yeastdownloads.org are using a bad SSL certificate. I guess they'll fix it eventually.
Answers.UserDisplayName: terdon
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-11-06T16:43:28.647Z
Answers.LastActivityDate: 2017-11-06T16:43:28.647Z
Answers.UserDisplayName: terdon
Answers.Body: <p>I am unaware of any "official" or gold-standard UTR annotations in <em>S. cerevisiae</em>.</p>
  
  <p>One option is to <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39128" rel="noreferrer">use the annotations</a> from the TIF-Seq publication (<a href="https://www.nature.com/nature/journal/v497/n7447/full/nature12121.html" rel="noreferrer"><strong>Pelechano et al. 2013</strong></a>).</p>
  
  <p>The <code>GSE39128_tsedall.txt.gz</code> file contains the major isoforms identified. It would be up to you to computational associate each transcript with a given gene. It is also up to you to determine which major isoforms are present in your dataset. Furthermore based on my own experience there is often a significant number of discrepancies between what I see in an NGS dataset (e.g. RNA-Seq) and what is called as a possible isoform in these annotations. However, a lot of this could be related to the inherent technological limitations of the method.</p>
  
  <p>If you look at the SGD genome browser they provide some additional UTR annotations. Derived from <a href="http://science.sciencemag.org/content/320/5881/1344" rel="noreferrer"><strong>Nagalakshmi et al. 2008</strong></a>.</p>
  
  <p>You can find the relevant annotations for those UTR's in their supplemental data section. The file is <code>1158441_tables_s2_to_s6.zip</code> and inside you will find <em>TableS4</em> which seems to contain what you seek.</p>
  
  <p>There might be more resources but these are the two main ones I'm aware of.</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-11-06T13:28:04.930Z
Answers.LastActivityDate: 2017-11-06T14:04:50.190Z
Answers.LastEditDate: 2017-11-06T14:04:50.190Z
Answers.UserDisplayName: story
Body: <p>I am working on a project in which I need to compute several parameters (such GC content and length) of 5'UTR and 3'UTR sequences of <em>Saccharomyces cerevisiae</em> yeast genes.</p>
  
  <p>The problem is finding a proper annotation for these regions in yeast. I have tried with BiomaRt and these sequences are not available for yeast. I have also tried with UCSC table browser to obtain a BED file with 5'UTR or 3'UTR sequences but it is returning only coordinates of tRNAs, pseudogenes, ncRNAs.</p>
  
  <p>In summary, <strong>is there a straight-forward way to obtain an annotation for 5'UTR and 3'UTR regions in <em>Saccharomyces cerevisiae</em> yeast</strong>?</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-11-06T12:58:50.490Z
Comments.Text: Sorry, is for Saccharomyces cerevisiae. I am going to edit the question just in case.
Comments.UserDisplayName: jxx_fa
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-11-06T17:15:26.350Z
Comments.Text: isn't there an equivalent of AceView for Yeast ? https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html
Comments.UserDisplayName: Yann TM
Tags: <sequence-annotation><bed><gtf>
Title: 5'UTR and 3'UTR annotation in yeast
ThreadText: # 5'UTR and 3'UTR annotation in yeast
  
  (Asked by: username_0 on 2017-11-06)
  
  I am working on a project in which I need to compute several parameters (such GC content and length) of 5'UTR and 3'UTR sequences of *Saccharomyces cerevisiae* yeast genes.
  
  The problem is finding a proper annotation for these regions in yeast. I have tried with BiomaRt and these sequences are not available for yeast. I have also tried with UCSC table browser to obtain a BED file with 5'UTR or 3'UTR sequences but it is returning only coordinates of tRNAs, pseudogenes, ncRNAs.
  
  In summary, **is there a straight-forward way to obtain an annotation for 5'UTR and 3'UTR regions in *Saccharomyces cerevisiae* yeast**?
  
  **Tags:** sequence-annotation, bed, gtf
  
  > **Comments:**
  > **username_0**: Sorry, is for Saccharomyces cerevisiae. I am going to edit the question just in case.  
  > **username_1**: isn't there an equivalent of AceView for Yeast ? https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_4 on 2017-11-06. Score: 9 | Accepted answer
  
  I am unaware of any "official" or gold-standard UTR annotations in *S. cerevisiae*.
  
  One option is to [use the annotations](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39128) from the TIF-Seq publication ([**Pelechano et al. 2013**](https://www.nature.com/nature/journal/v497/n7447/full/nature12121.html)).
  
  The `GSE39128_tsedall.txt.gz` file contains the major isoforms identified. It would be up to you to computational associate each transcript with a given gene. It is also up to you to determine which major isoforms are present in your dataset. Furthermore based on my own experience there is often a significant number of discrepancies between what I see in an NGS dataset (e.g. RNA-Seq) and what is called as a possible isoform in these annotations. However, a lot of this could be related to the inherent technological limitations of the method.
  
  If you look at the SGD genome browser they provide some additional UTR annotations. Derived from [**Nagalakshmi et al. 2008**](http://science.sciencemag.org/content/320/5881/1344).
  
  You can find the relevant annotations for those UTR's in their supplemental data section. The file is `1158441_tables_s2_to_s6.zip` and inside you will find *TableS4* which seems to contain what you seek.
  
  There might be more resources but these are the two main ones I'm aware of.
  
  
  ---
  
  ### Answer by username_2 on 2017-11-06. Score: 7
  
  I found the following two files in <https://downloads.yeastgenome.org/sequence/S288C_reference/>:
  
  * [SGD\_all\_ORFs\_3prime\_UTRs.fsa](https://downloads.yeastgenome.org/sequence/S288C_reference/SGD_all_ORFs_3prime_UTRs.fsa)
  * [SGD\_all\_ORFs\_5prime\_UTRs.fsa](https://downloads.yeastgenome.org/sequence/S288C_reference/SGD_all_ORFs_5prime_UTRs.fsa)
  
  According to the README files in the same directory, these are (the README for the 5' file is equivalent):
  
  > SGD\_all\_ORFs\_3prime\_UTRs.README
  >
  > Information about the SGD\_all\_ORFs\_3prime\_UTRs.fsa file.
  >
  > This file contains sequences for predicted 3' UTR sequences for all
  > characterized, uncharacterized and dubious ORFs in S288c.
  >
  > 3' UTR coordinates were retrieved from YeastMine
  > (yeastmine.yeastgenome.org) on July 3, 2017 using the stop coordinates
  > of both the predicted transcript and gene sequences. A BED file with
  > these coordinates was made. BED files were fixed on Sept 22, 2017 to
  > account for strandedness. Sequences were batch downloaded again in
  > FASTA format from USCS Genome Table Browser on Sept 22, 2017
  > (<https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=604915183_aUc9FZ1vwyAccGti1uI0wteYEM7x>)
  >
  > File created: 2017-08-25
  
  Those therefore seem to be the 3' and 5' UTR sequences of all yeast genes in FASTA format and should be exactly what you need.
  
  > **Comments:**
  > **username_3**: The link is broken  
  > **username_2**: @username_3 yes, apparently yeastdownloads.org are using a bad SSL certificate. I guess they'll fix it eventually.  
  
  ---
  
  