Can anyone suggest a software to identify the introns and exons present in a sequence? The sequence is not available in NCBI.
So, you can use the following site:http://genome.ucsc.edu/. Do you know it?
You click in "Table" and in the option "region" you choose "position", write the gene name (i.e: FASL) and click in "lookup". So, You choose the gene, preferentially RefSeq, and click in output at the end of the page.
If you have some questions about it I can explain better.
I hope I have helped you.
For genomes present in Ensembl, how about this?
http://www.ensembl.org/Homo_sapiens/Transcript/Sequence_cDNA?db=core;g=ENSG00000111640;r=12:6643093-6647537;t=ENST00000229239
It shows you the exons in alternating colors. You could also modify the display to also show introns.
If you have sequence to use as training, you can try Augustus (http://bioinf.uni-greifswald.de/augustus/) for gene prediction, otherwise in general you can translate the six frames in your sequence with any ORF finder and look for splice signals in the borders of exons. Do you have mRNA sequences (EST, NGS) to use to improve your prediction? any gene homology in other related species?
So, you can use the following site:http://genome.ucsc.edu/. Do you know it?
You click in "Table" and in the option "region" you choose "position", write the gene name (i.e: FASL) and click in "lookup". So, You choose the gene, preferentially RefSeq, and click in output at the end of the page.
If you have some questions about it I can explain better.
I hope I have helped you.
Have you tried ORF finder? http://www.ncbi.nlm.nih.gov/gorf/gorf.html
BLAST (blastn) the sequence against Genbank (nr). There should be conservation of intron-exon structure between closely related organisms.
GenScan might be fine. Its a online tool from the HUSAR bioinformatic department of the DKFZ in Heidelberg.
For the gene prediction the best tool is Augustus(http://bioinf.uni-greifswald.de/augustus/submission). If your species is already in the list (so the tool is trained for it), you have only to submit the sequence and press te button. If the tool is not yet trained for your species, select any closely related species, better take 2 or 3 of them. In mot cases thisgives more or less reliable results.
If you have the cDNA sequence and the genomic sequence you can use SPLINE at NCBI to compare. It finds the correct exon/intron junctions.
http://www.ncbi.nlm.nih.gov/sutils/splign/splign.cgi
Blast 2 sequences will find approximate exons but will not correctly identify the junctions.
I you have the cDNA sequence and also the genomic you can use spidey from NCBI.
http://www.ncbi.nlm.nih.gov/spidey/index.html
Dear Raksha,
Now Spidey is superceded by Splign for computing cDNA-to-Genomic, or spliced sequence alignments using an algorithm which identifies possible gene duplications, and a refined alignment algorithm recognizing introns and splice signals.
Please see here:
https://www.ncbi.nlm.nih.gov/sutils/splign/splign.cgi
https://www.ncbi.nlm.nih.gov/sutils/splign/splign.cgi?textpage=documentation
or here:
ftp://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/splign/linux-i64/
Please see my recently answer and the answers from the other colleagues. There a lot of software solutions!
You can use GENSATT, SPSS or
NTSYS, http://www.exetersoftware.com/cat/ntsyspc/ntsyspc.html
to do diversity analysis using plant taxanomic and morphologicalmarkers
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology