Answers.Body: <p>Col-0 is, to my knowledge, the standard reference Arabidopsis thaliana ecotype, so the easiest way to get the sequences for all genes is to just download them from Ensembl. The nucleotide sequences are <a href="ftp://ftp.ensemblgenomes.org/pub/release-46/plants/fasta/arabidopsis_thaliana/cdna/" rel="nofollow noreferrer">available here</a> and the protein sequences <a href="ftp://ftp.ensemblgenomes.org/pub/release-46/plants/fasta/arabidopsis_thaliana/pep/" rel="nofollow noreferrer">here</a>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-12T16:31:51.310Z
Answers.LastActivityDate: 2020-03-12T16:31:51.310Z
Answers.UserDisplayName: Devon Ryan
Answers.Body: <p>For RefSeq data, go to <a href="https://www.ncbi.nlm.nih.gov/" rel="nofollow noreferrer">NCBI homepage</a> and search for <code>Arabidopsis Col-0 genome</code>. Click on the 'Get Data' button in the result box and you will be directed to the <a href="https://www.ncbi.nlm.nih.gov/datasets/genomes/?acc=GCF_000001735.4" rel="nofollow noreferrer">NCBI Datasets</a> portal with the latest RefSeq assembly selected. Click on the blue 'Download' button, uncheck the genome and GFF3 files from list, check transcript and protein FASTA files from the list and download data. </p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-26T12:02:00.313Z
Answers.LastActivityDate: 2020-04-26T12:02:00.313Z
Answers.UserDisplayName: vkkodali
Body: <p>I want to collect all isoforms of all genes (Fasta/Fastq file of nucleotide and protein sequences) Arabidopsis Col-0. I am wondering if there is a straightforward way to download the file from any database.</p>
  
  <p>I am new to sequence analysis, so I apologize if asking a very basic question. </p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-05T23:02:32.440Z
Comments.Text: Do you want a single gene? Look at Uniprot then
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-06T02:00:43.940Z
Comments.Text: IMO you are into alternate splicing sites, more proteomics and RNAseq than genomics.
Comments.UserDisplayName: M__
Tags: <rna-seq><phylogenetics><sequence-analysis><phylogeny><isoform>
Title: Download sequences of isoforms
ThreadText: # Download sequences of isoforms
  
  (Asked by: username_0 on 2020-03-05)
  
  I want to collect all isoforms of all genes (Fasta/Fastq file of nucleotide and protein sequences) Arabidopsis Col-0. I am wondering if there is a straightforward way to download the file from any database.
  
  I am new to sequence analysis, so I apologize if asking a very basic question.
  
  **Tags:** rna-seq, phylogenetics, sequence-analysis, phylogeny, isoform
  
  > **Comments:**
  > **username_1**: Do you want a single gene? Look at Uniprot then  
  > **username_2**: IMO you are into alternate splicing sites, more proteomics and RNAseq than genomics.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_3 on 2020-03-12. Score: 1
  
  Col-0 is, to my knowledge, the standard reference Arabidopsis thaliana ecotype, so the easiest way to get the sequences for all genes is to just download them from Ensembl. The nucleotide sequences are [available here](ftp://ftp.ensemblgenomes.org/pub/release-46/plants/fasta/arabidopsis_thaliana/cdna/) and the protein sequences [here](ftp://ftp.ensemblgenomes.org/pub/release-46/plants/fasta/arabidopsis_thaliana/pep/).
  
  
  ---
  
  ### Answer by username_4 on 2020-04-26. Score: 0
  
  For RefSeq data, go to [NCBI homepage](https://www.ncbi.nlm.nih.gov/) and search for `Arabidopsis Col-0 genome`. Click on the 'Get Data' button in the result box and you will be directed to the [NCBI Datasets](https://www.ncbi.nlm.nih.gov/datasets/genomes/?acc=GCF_000001735.4) portal with the latest RefSeq assembly selected. Click on the blue 'Download' button, uncheck the genome and GFF3 files from list, check transcript and protein FASTA files from the list and download data.
  
  
  ---
  
  