More posts like this
-
Using Lastz aligner
written by Diego 11Hi, I am trying to align two genomes (700Mb) using Lastz. The problem is that although my command is running fine and I am getting …
-
.axt formats for pairwise alignments and how to convert to paml
written by spiral01 11I am currently trying to calculate rates of substitution in humans, using the human-chimpanzee pairwise alignment found here: http://hgdownload.soe.ucsc.edu/goldenPath/hg38/vsPanTro6/ My problem is that the alignment …
-
What is the best tool for generating Multiple sequence alignment (MSA) of fasta sequences ?
written by sunnykevin97 100HI, Could anyone suggest me the best tool, for performing multiple sequence alignment among fasta sequences. Should generate output in MAF (Multiple alignment format) ?? …
-
how can I convert the gff3 file into EMBL format??
written by Jerryliu 1Hi! A sequence alignment software I use requires me to hand in the gene annotation file in EMBL format, but I only have the file …
-
Multiple Sequence Alignment of Bacterial Genomes
written by Optimist 19Hi All, I have a couple of queries regarding Multiple Sequence Alignment. 1. I have downloaded Genomes in fasta format from NCBI. Some are Complete …
-
convert sam format to axt Format
written by midox 29<p>hello,<br /> I would like to convert my sam file <strong>(.sam)</strong> to another type is <strong>.axt</strong> format.<br /> i used <em>BWA </em>for alignement but the …
-
covert STOCKHOLM alignment to FASTA alignment
written by venu 714Hello, I've generated a multiple sequence alignment pf protein sequences with HMMER suite. The possible output formats with this are SELEX and STOCKHOLM. Is there …
-
How to Convert Fasta format or .aln format to PIR format ??
written by rajkishore.ouatbi 1I have fasta format. Can anyone say how to convert the fasta format to pir format. Also, I have clustalw alignment format, then how to …
-
How Do You Convert A Sam/Bam File To A Psl Or Axt Format?
written by lp364 2<p>I am trying to make a chain file to use in liftOver and these can be made using PSL or AXT files. My current data …
-
Duplicate Chain Error When Running Nettoaxt
written by Nathan Harmston 113<p>Hi everyone, </p> <p>So I'm trying to generate some axtFiles from a whole-genome alignment - using this walkthrough <a href='http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto'>http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto</a> ... however at the stage …