Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • cewells
    replied
    Thanks westerman -- we modified for the new blast+ as below --

    1) makeblastdb -in Trinity.fasta -dbtype nucl -parse_seqids -out TrinityBlast -title "All contigs"
    2) blastn -query myfile.fa -db TrinityBlast -out myfile.out
    3) same
    4) blastdbcmd -db TrinityBlast -entry myid > found.fa

    Leave a comment:


  • westerman
    replied
    Local db. Using the older version of blast (although blast+ is similar):

    1) formatdb -i Trinity.fasta -p F -o T
    2) blastall -p blastn -d Trinity.fasta -i myfile.fa -o output.blastn
    3) manually look at output.blastn to figure out the id of the matching contig
    4) fastacmd -d Trinity.fasta -s myid > found.fa

    Leave a comment:


  • Daisy-Fu
    replied
    Originally posted by westerman View Post
    Blast of your Trinity contigs against the partial sequence? Should be fast enough and sensitive enough to pick up the contig(s). Or am I missing something obvious here?
    Hey, Westerman in Purdue, thank you for you replying.
    Are you talking about build a local db or www-blast something like that?

    Leave a comment:


  • westerman
    replied
    Blast of your Trinity contigs against the partial sequence? Should be fast enough and sensitive enough to pick up the contig(s). Or am I missing something obvious here?

    Leave a comment:


  • How to dig out single particular gene from assembled contigs

    Sorry if this question has been asked before. I just did a RNA-seq of a plant parasitic nematode species, and assembled 50,000 contigs by Trinity.
    I would like to dig out a full-length sequence of endoglucanase gene, and do some protein structure prediction like that. Partial sequence of this gene was available through previous degenerate PCR. Does anybody know a easy and simple way to do it?
    Thanks a lot.

Latest Articles

Collapse

  • seqadmin
    Recent Advances in Sequencing Analysis Tools
    by seqadmin


    The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
    05-06-2024, 07:48 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 02:06 PM
0 responses
7 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-14-2024, 07:03 AM
0 responses
27 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-10-2024, 06:35 AM
0 responses
47 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-09-2024, 02:46 PM
0 responses
59 views
0 likes
Last Post seqadmin  
Working...
X