Answers.Body: <p>What in particular do you need from that format? If it's just the pipes separating fields, then that's what GENCODE does with their FASTA format:</p>
  <p><a href="https://www.gencodegenes.org/human/" rel="nofollow noreferrer">https://www.gencodegenes.org/human/</a></p>
  <pre><code>&gt;ENST00000417138.1|ENSG00000223608.1|OTTHUMG00000086672.1|OTTHUMT00000194833.1|DSCR4-IT1-201|DSCR4-IT1|424|lncRNA|
  AGTTCCTTCTTAGGTATGGGGATCTCAGCAGTTTCATTTCAGTGGCCACAGCTTGGGAAA
  CAGACTTCTCCCAATATCAAAGGGAATCAAGTCCCCCTTTTTTTCTCCAGGCCTCGGTCT
  GCAGCATCTGTGATGCATCAGACTGCAATTGAGCCATCCAAGGATACAATCATAGCAATC
  AAAAAGAGTGACTGGAGGAAGAAGGAAATGAACATAGAAGAGGAAAAAAAAGAAATCTTG
  </code></pre>
  <p>Bear in mind that it's Ensembl IDs rather than NCBI IDs.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-12-16T06:05:50.163Z
Answers.LastActivityDate: 2024-12-16T06:05:50.163Z
Answers.UserDisplayName: gringer
Body: <p>Some time ago, I worked with NCBI FASTA files--specifically human refseq files--that had record headers in a style and with information that is no longer used. For example, headers of this style</p>
  <pre><code>&gt;gi|46358415|ref|NM_005867.2| Homo sapiens Down syndrome critical region gene 4 (DSCR4), mRNA
  </code></pre>
  <p>have been replaced by those of this style</p>
  <pre><code>&gt;NM_005867.2 Homo sapiens Down syndrome critical region 4 (DSCR4), mRNA
  </code></pre>
  <p>For teaching and writing purposes, it would be great to have records in the first style.</p>
  <p>I'm particularly interested in human reference sequence transcripts, specifically a version of the files found in <a href="https://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot" rel="nofollow noreferrer">ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot</a> in which records have the style of the header shown far above. The final objective is to have students work with no longer publicly available data, as this would decrease the likelihood of existing solutions being out there. In addition, the old format is a little harder to process than the new one, which would inherently provide a challenge.</p>
  <p>Does anybody know if/where I could find them? I understand that current records wouldn't be available. I'm just looking for human refseq records in that style.</p>
  <p>Any help would be greatly appreciated!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-12-15T17:28:45.473Z
Comments.Text: What data do you need? The human refseq transcriptome specifically? Or any group of sequences that still have the gi etc? And can you explain what the final objective is? It seems odd to want to teach students to rely on a format that is unlikely to be available. Would it make more sense to just create this by mapping the refseq IDs to the corresponding gi number yourself? And why would you want the gi if you have the refseq?
Comments.UserDisplayName: terdon
Tags: <fasta><ncbi><multi-fasta>
Title: FASTA Files in the old style
ThreadText: # FASTA Files in the old style
  
  (Asked by: username_0 on 2024-12-15)
  
  Some time ago, I worked with NCBI FASTA files--specifically human refseq files--that had record headers in a style and with information that is no longer used. For example, headers of this style
  
  ```
  >gi|46358415|ref|NM_005867.2| Homo sapiens Down syndrome critical region gene 4 (DSCR4), mRNA
  
  ```
  
  have been replaced by those of this style
  
  ```
  >NM_005867.2 Homo sapiens Down syndrome critical region 4 (DSCR4), mRNA
  
  ```
  
  For teaching and writing purposes, it would be great to have records in the first style.
  
  I'm particularly interested in human reference sequence transcripts, specifically a version of the files found in [ftp.ncbi.nih.gov/refseq/H\_sapiens/mRNA\_Prot](https://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot) in which records have the style of the header shown far above. The final objective is to have students work with no longer publicly available data, as this would decrease the likelihood of existing solutions being out there. In addition, the old format is a little harder to process than the new one, which would inherently provide a challenge.
  
  Does anybody know if/where I could find them? I understand that current records wouldn't be available. I'm just looking for human refseq records in that style.
  
  Any help would be greatly appreciated!
  
  **Tags:** fasta, ncbi, multi-fasta
  
  > **Comments:**
  > **username_1**: What data do you need? The human refseq transcriptome specifically? Or any group of sequences that still have the gi etc? And can you explain what the final objective is? It seems odd to want to teach students to rely on a format that is unlikely to be available. Would it make more sense to just create this by mapping the refseq IDs to the corresponding gi number yourself? And why would you want the gi if you have the refseq?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2024-12-16. Score: 0
  
  What in particular do you need from that format? If it's just the pipes separating fields, then that's what GENCODE does with their FASTA format:
  
  <https://www.gencodegenes.org/human/>
  
  ```
  >ENST00000417138.1|ENSG00000223608.1|OTTHUMG00000086672.1|OTTHUMT00000194833.1|DSCR4-IT1-201|DSCR4-IT1|424|lncRNA|
  AGTTCCTTCTTAGGTATGGGGATCTCAGCAGTTTCATTTCAGTGGCCACAGCTTGGGAAA
  CAGACTTCTCCCAATATCAAAGGGAATCAAGTCCCCCTTTTTTTCTCCAGGCCTCGGTCT
  GCAGCATCTGTGATGCATCAGACTGCAATTGAGCCATCCAAGGATACAATCATAGCAATC
  AAAAAGAGTGACTGGAGGAAGAAGGAAATGAACATAGAAGAGGAAAAAAAAGAAATCTTG
  
  ```
  
  Bear in mind that it's Ensembl IDs rather than NCBI IDs.
  
  
  ---
  
  