Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 3'UTR seq extraction

    Hello,
    I am new to the forum and this is my first post here !

    I have a pair of fasta sequence files one having several CDS sequences (file X) and the other with several full length transcript sequences (file Y).
    The file (file X) with CDS sequence have entries as follows:
    >ABCD (40..120)
    …………the sequence……………….
    This goes on for another 200 different gene entries

    The file (file Y) with the full length transcript sequence have entries as follows:
    >ABCD (1..700)
    …………the sequence……………….
    And this also goes on for another 200 different gene entries.

    The ABCD implies a gene name which is of course identical in both the fasta files. Hence the sequence is also identical in between coordinates 40..120 for both sets.
    I want to extract the 3’ UTR sequences from all the fasta sequence entries that are in the full transcript file. So basically, I am trying to come up with a script that will allow me to extract the sequence from the full transcript file right after where the CDS sequence ends. So in the above example I am trying to get the sequence between (121 ..700) for gene ABCD from the full transcript fasta file. I am trying to make the script so that it loops through the entire file for all the 200 gene entries.

    I am primarily using bash and little of perl.
    Any help will be most appreciated.

    Thanks and regards!

Latest Articles

Collapse

  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
11 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
51 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
68 views
0 likes
Last Post seqadmin  
Working...
X