Extracting subalignments from MAF file

Hello, dear colleagues,

I need to extract subalignments of mRNA from MAF format file. I have .MAF multiz alignment and .GFF3 file for hg19, so how can I possibly do it?

Thanks in advance

maf

• 2,464 views • link

written 9.9 years ago by prosvirov.k •

Have a look at https://github.com/bxlab/bx-python

• 1 views • link

written 9.9 years ago by Peter

0 answers

No answers yet.

More posts like this

Is hg38 on the multiz 30-way alignment inaccurate?
written 3.2 years ago by Daniel •

Hello, I have a general question: Is it possible that the multiz 30-way alignment is inaccurate? I am looking for specific hg38 sequences in the …
How extract specific SNP position from the bed file-Bedtools
written 3.2 years ago by LionisOne •

I have one bed file with start and end coordinate (range in bed format). I need to extract a specific position from this range bed …
Using the 27-primates UCSC Multiz Alignment
written 3.3 years ago by Daniel •

Hello, I am attempting to use the 27-primates UCSC multiz alignment data so that I can find an orthogonal sequence (across different mammals) to a …
How to convert trinotate results into GFF3
written 3.7 years ago by arshad1292 •

Hello, I ran trinotate and obtained "trinotate_annotation_report.xls" file that I want to convert to GFF3 format. Can anyone please let me know how can I …
Slicing Genbank File by range
written 5.5 years ago by kamel •

Dear colleagues, I have a genbank file annotated from a genome draft (contig_1 to contig_89). I'm interested in extracting only a region 20,500 to 21,500 …
Retrieve GFF3 file from Ensembl
written 7.1 years ago by jamesdong •

I have a bunch of Ensembl mRNA IDs of homologous genes from different species: ENSGACT00000003747,ENSMLUT00000000343,ENSMICT00000005631,......, I want to retrieve conresponding gff3 files respectively from ensembl …
how can I convert the gff3 file into EMBL format??
written 7.9 years ago by Jerryliu •

Hi! A sequence alignment software I use requires me to hand in the gene annotation file in EMBL format, but I only have the file …
Getting mRNAs coordinates and extracting subalignments
written 9.9 years ago by prosvirov.k •

Hello, dear colleagues, I need to extract the alignments of 5'UTR from multiple genome alignments in .msa format.My idea is too get the file containing …
Extracting promoter regions alignment
written 10.6 years ago by prosvirov.k •

Greetings, everyone! I`m trying to extract promoter regions alignment from UCSC Table Browser. I can get promoter regions for any species using output format as …
How can I upload a file that is larger than 50G on Galaxy?
written 10.8 years ago by sfpry •

I want to convert the MultiZ MAF file for chromosome 1 to FASTA format on Galaxy. The UCSC .maf file is about 67G, but the …