Thank you! How can I exclude isoforms?
• 0 views
•
link
written
by
fire_water
Batch Retrieval of Coding Sequences
Hello, I have a long list of human gene names (for example CFTR, ABCA1) and I want to retrieve the coding sequences for each gene. Does anyone know of a way to upload this list and retrieve the sequences in FASTA format?
• 3,010 views
•
link
updated
by
Ram
•
written
by
fire_water
•
written
by
fire_water
1 answer
You can get it out from Biomart. I think you want to get cDNA for gene, if you want to have isoforms sequences you can download gtf file from table browser export the knownGene as a GTF
grep -w 'CDS' in.gtf > out.gtf
Just get fasta sequence from gtf using bedops
• 0 views
•
link
updated
by
Ram
•
written
by
Manvendra Singh
•
written
by
Manvendra Singh
if you want to have one sequence per gene then you would need to have one isoform,
I would take the sequence from longest isoform .
• 0 views
•
link
written
by
Manvendra Singh
Log in to answer this question.
More posts like this
-
extract single contig from fasta file based on name?
written by goatsrunfaster •
-
Blast2GO : how to select only transcription factors
written by evafinegan •
-
Extract info on OMIM Phenotype
written by NB
-
Retrieve nt sequence of chloroplaste genes (NCBI query with gene name and taxon ID)
written by erica.fary •
-
Downloading sequences of genes related to a pathway in PlantCyc (or other cyc related databases) an…
written by ahmad.iut
-
Extract fasta sequences from a large file using a list of names
written by fhsantanna
-
3’UTR sequences for Saccharomyces Cerevisiae (yeast)
written by fire_water
-
Perl Script To Retrieve All Orf?
written by Adrian Pelin
-
Retrieve One Coding Sequences For Each Gene
written by Mohammad Reza Bakhtiarizadeh
-
Ka/Ks Ratio To Detect Selection (Nonsynonmous To Synonymous) In Dnasp
written by User 7433 •
