Answers.Body: <p>It's possible that <a href="https://blast.ncbi.nlm.nih.gov/moleblast/moleblast.cgi" rel="nofollow noreferrer">MOLE-BLAST</a> could help for you:</p>
  <blockquote>
  <p>MOLE-BLAST is an experimental tool that helps taxonomists find closest database neighbors of submitted query sequences. It computes a multiple sequence alignment (MSA) between the query sequences along with their top BLAST database hits, and generates a phylogenetic tree. Query sequences in the tree are denoted with highlighted node labels. If the input sequences come from different genes or loci, MOLE-BLAST can cluster them and compute an MSA and a phylogenetic tree for each locus separately. This tool may eventually be incorporated into our supported suite of BLAST applications based on the feedback we receive.</p>
  </blockquote>
  <p>I haven't actually used MOLE-BLAST, but I have used <a href="https://blast.ncbi.nlm.nih.gov/smartblast/" rel="nofollow noreferrer">Smart BLAST</a>, which does a somewhat similar phylogenetic search (although on a restricted diverse taxonomic set) for protein queries.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-03-20T19:10:46.747Z
Answers.Text: thank you! I'll try that.
Answers.UserDisplayName: Jacob
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-03-16T18:55:01.423Z
Answers.LastActivityDate: 2023-03-16T18:55:01.423Z
Answers.UserDisplayName: gringer
Body: <p>Given a set of genes in a FASTA-formatted file, for example: <code>exFasta.fa</code>, what is the best way to determine how well conserved the genes in that file are among an order of organisms, for example: Orthoptera?</p>
  <p>BLAST is an obvious option, but I am not sure that it is the most efficient way considering there are likely thousands of organisms in that order. OrthoFinder also comes across as a valid option, but I am not sure how to implement such a thing considering the required inputs.</p>
  <p>Any advice would be greatly appreciated!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-03-16T12:43:42.843Z
Comments.Text: Are these annotated, known genes? Or do you also need to detect/identify the potential homologs in the target species?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-03-17T21:28:45.367Z
Comments.Text: Orthoptera (grasshoppers, crickets, locust) will be annotated (mostly). What they want to do is skim the draft genomes of Orthoptera. I like @gringers answer, it's a good one. As a project it would work.
Comments.UserDisplayName: M__
Tags: <python><blast><blastp><orthofinder>
Title: Given a FASTA file with a set of genes, how do I determine that set's conservation among a genetic order?
ThreadText: # Given a FASTA file with a set of genes, how do I determine that set's conservation among a genetic order?
  
  (Asked by: username_0 on 2023-03-15)
  
  Given a set of genes in a FASTA-formatted file, for example: `exFasta.fa`, what is the best way to determine how well conserved the genes in that file are among an order of organisms, for example: Orthoptera?
  
  BLAST is an obvious option, but I am not sure that it is the most efficient way considering there are likely thousands of organisms in that order. OrthoFinder also comes across as a valid option, but I am not sure how to implement such a thing considering the required inputs.
  
  Any advice would be greatly appreciated!
  
  **Tags:** python, blast, blastp, orthofinder
  
  > **Comments:**
  > **username_1**: Are these annotated, known genes? Or do you also need to detect/identify the potential homologs in the target species?  
  > **username_2**: Orthoptera (grasshoppers, crickets, locust) will be annotated (mostly). What they want to do is skim the draft genomes of Orthoptera. I like @gringers answer, it's a good one. As a project it would work.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2023-03-16. Score: 2
  
  It's possible that [MOLE-BLAST](https://blast.ncbi.nlm.nih.gov/moleblast/moleblast.cgi) could help for you:
  
  > MOLE-BLAST is an experimental tool that helps taxonomists find closest database neighbors of submitted query sequences. It computes a multiple sequence alignment (MSA) between the query sequences along with their top BLAST database hits, and generates a phylogenetic tree. Query sequences in the tree are denoted with highlighted node labels. If the input sequences come from different genes or loci, MOLE-BLAST can cluster them and compute an MSA and a phylogenetic tree for each locus separately. This tool may eventually be incorporated into our supported suite of BLAST applications based on the feedback we receive.
  
  I haven't actually used MOLE-BLAST, but I have used [Smart BLAST](https://blast.ncbi.nlm.nih.gov/smartblast/), which does a somewhat similar phylogenetic search (although on a restricted diverse taxonomic set) for protein queries.
  
  > **Comments:**
  > **username_0**: thank you! I'll try that.  
  
  ---
  
  