Question: Alternate Transcripts Paralogs
1
gravatar for aj123
6.7 years ago by
aj12370
United States
aj12370 wrote:

Hello,

I have a few doubts related to how the best way is to go about finding these:

  1. Finding unique regions when you compare various transcripts of a gene in one organism.
  2. Finding evidences for a particular transcript.
  3. Finding the % identity IN NCBI PROTEIN database for a particular sequence taken from uniprot. i.e i blast a protein sequence in uniprot database and get the paralogs for that along with percent identity. then i want to find the corresponding sequences for those paralogs in NCBI protein and find the %ID for my query sequence against those NCBI protein sequences. i tried ID mapping in uniprot and it gives me the corresponding IDs. but when i blast my query sequence against these IDs the %identity is way off from the %ID uniprot gives me.

any help/suggestions would be greatly appreciated.

gene ncbi uniprot • 1.9k views
ADD COMMENTlink modified 6.7 years ago • written 6.7 years ago by aj12370

I am a bit confused. Do you mean you want to differentiate between alternative isoforms and paralogs?

ADD REPLYlink written 6.7 years ago by Damian Kao15k

No, i just want to find orthologs and paralogs for a particular gene from a particular species (human). Apart from this, I also want to find alternate transcripts for a gene in human.

ADD REPLYlink modified 6.6 years ago • written 6.6 years ago by aj12370
1
gravatar for JC
6.7 years ago by
JC7.7k
Mexico
JC7.7k wrote:
  1. I assume that you want to identify isoform-specific exons for a gene, in that case, you need to overlap your annotations, and select the regions transcript-specific. You can do that with R:bioconductor and IRanges.
  2. Evidence of what? expression? protein? conservation?
  3. Are you using the same blast parameters? if the parameters are the same, the alignments must be similar.
ADD COMMENTlink written 6.7 years ago by JC7.7k

@JC Thanks so much for your reply.

1) is there a way to do this using just online bioinfo databases like NCBI, Ensembl etc with out using IRanges? also, how would i a) find the annotations for a transcript b)go aobut overlapping my annotations c)select the regions which are transcript specific? i mean how would i know a region is transcript specific?

2) evidence of expression

3)yes, all blast parameters used are standard ones. im not sure still how/why this is happening

ADD REPLYlink written 6.7 years ago by aj12370

1) and 2) depends on your model, human? mouse? 3) did you check if the alignments are the same? I'm thinking if you have 2 sequences, A with 100aa and B with 200aa, and you found a common alignment of 50aa, when you compare A->B the %ID is be 50% (based on A) but B->A is 25% (based on B)

ADD REPLYlink written 6.7 years ago by JC7.7k

Im using Human. Im not sure how you mean w.r.t the second part. im blasting always in a standard format. i.e original sequence vs. subject sequences. Still a little confused w.r.t finding the alternate transcripts for a gene.

ADD REPLYlink written 6.6 years ago by aj12370

Default (standard) blast parameters differ between NCBI and UniProt blast sites. You have to be very careful about each setting.

ADD REPLYlink written 6.5 years ago by Jerven640
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