I'm looking for help with running RepeatMasker on RepeatScout output. The documentation just says
"RepeatMasker is run on the sequence...
14 results in 0.0026 seconds.
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RepeatScout and RepeatMasker
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Biopython pdb.DSSP fasta
Hi everyone!
I`ve a trouble with run DSSP module with protein in fasta format. Is it possible to run DSSP from biopython interface with sequence... -
Extraction of a portion of a fasta header
Hi,
I have a multi fasta file whose header is like below,
">WLPTB:00031:00193;size=517;"
now... -
Introduction
I am an undergraduate student at UNLV and am taking a Bioinformatics class. We just recently had our exomes sequenced and were given the fastq file that... -
Getting sequences from multiprotein .faa file?
Anyone have a favorite command-line method for grabbing specific entries from a FASTA Amino Acid (.faa) file? I have a list of sequences that I'd like... -
construct DNA sequence based on variation and human reference
The 1000 genome project provides us information about "variation" of thousands people's DNA sequence against the human reference DNA sequence.... -
Download Human Genome
I want to download assembled human genome from nbci site to calculate some statistics on it. I found GRCh37 in the link below
http://www.ncbi.... -
Meaning of 1KGP FASTA file headers
I downloaded the 1KGP fasta file from ftp://ftp.1000genomes.ebi.ac.uk/vol1...cal/reference/. 1:1:249250621 means chr1:1-249250621 obviously. What... -
[bedtools][fastaFrombed] could not stat file
I have a fasta file rn4.fa with the rat genome and also a fai file rn4.fa.fai which I generated with samtools faidx. I want to extract fasta from bed... -
1000genomes SRR107002.filt.fastq.gz bad format?
The first few lines of ftp://ftp.1000genomes.ebi.ac.uk/vol1....filt.fastq.gz are:
@SRR010375.1 VAB_S0083_BCM_20080731_1_Pilot_2_YRI_Fragment2199_1705_1499... -
Any script to format headers in fasta files?
I have a 47GB file to parse. The sequences are in following format:
>TSCS_00041 gene0EA_12345_rframe2_ORF
MLAATHYYKFAIRRLFPLLKDTICASYSISIKHHENFMALSNMPKIWEDVEVDGNNMQWTRFQTTPVMPVYFIAAGVFNLSFITNWNTKLLYRKDILPYMTFAYNVAKNIAWFLSHIRKTKITNHI... -
keeping heterozygote information in fasta format from .bam files
Hi everyone,
I’m using the GATK “FastaAlternateReferenceMaker” walker to pull out candidate gene sequences from my .bam files. What... -
cuffmerge failed
any idea about this failure? how to make fasta have the same length? and what does this mean? thank you!
[Wed Sep 28 20:19:22 2011] Beginning... -
Appropriate Reference Format
Hello,
I am trying to deal with some targeted resequencing data. I have a subset of hg19 that I targeted with a SureSelect Capture array...
