Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Avazeh
    replied
    Thank you both, will try them out

    Leave a comment:


  • ishmael
    replied
    If all sequences are form human, I would suggest use reciprocal liftover approach.
    1. download liftover program from UCSC.
    2. download liftover chain files: both of human to gorilla and gorilla to human. You can find them under the genome file download pages.
    3. mapping the sequences to human genome, and get the coordination in bed format.
    4. convert human bed to gorilla genome by liftover, allow multiple convertion.
    5. convert the converted gorilla bed file back to human genome, also multiple loci allowed.
    6. filtered the results that the gorilla and human could be converted reciprocally.
    That's the protocol I think relatively reliable.

    Leave a comment:


  • dpryan
    replied
    Originally posted by Avazeh View Post
    I need to align my regions to Gorilla's 2011 built, gorGOR3, in which the supercontigs are resolved into chromosomes.
    gorGOR3 is available from Ensembl, so I would recommend just downloading the fasta files and aligning to them.

    Leave a comment:


  • Avazeh
    replied
    Sure:

    I have 400 human seqs, each between 2kb to 4kb. I need to map them to Gorilla and Chimp and then look for motifs in the extended alignments found. Submitted the regions to UCSC table browser and downloaded conservation in Comparative Genome group, using Multiz Align option to get the sequences in the alignments too. Unfortunately these alignment are just available on gorGOR1 which is the first Gorilla build and contains contig number rather than chromosome number! So I really don't know where on Gorilla genome they hit and cannot extend it to do motif analysis

    I need to align my regions to Gorilla's 2011 built, gorGOR3, in which the supercontigs are resolved into chromosomes.

    Any help is appreciated

    Leave a comment:


  • ishmael
    replied
    Would you mind to provide more details?
    What's the tool you used to do the aignment? liftover?
    What's the nature of your data?

    Leave a comment:


  • Avazeh
    started a topic Tool for Human to Gorilla alignment

    Tool for Human to Gorilla alignment

    Hi all,

    I have 400 human seqs to align to Gorilla and Chimp. Tried UCSC and got a useful alignment for Chimp but the Gorilla one has supercontigs rather than chromosome numbers

    I have to add 2kb to the aligned seqs and then pass to another tool. But his is not possible with just having supercontigs numbers! So I am looking for an alternative.

    Any idea or thought would be much appreciated,
    Avazeh

Latest Articles

Collapse

  • seqadmin
    Essential Discoveries and Tools in Epitranscriptomics
    by seqadmin




    The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
    04-22-2024, 07:01 AM
  • seqadmin
    Current Approaches to Protein Sequencing
    by seqadmin


    Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
    04-04-2024, 04:25 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 08:47 AM
0 responses
12 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
60 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
59 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
54 views
0 likes
Last Post seqadmin  
Working...
X