User: HZZ0036

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HZZ00360
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Posts by HZZ0036

<prev • 11 results • page 1 of 2 • next >
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Comment: C: MCScanX result problem
... Here is the script for blastall: blastp -db /mcScanX/goose_maize -query /mcScanX/goose_maize.fa -out /mcScanX/goose_maize.blast -evalue 1e-10 -outfmt 6 -num_threads 20 -num_alignments 5 ...
written 21 hours ago by HZZ00360
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Comment: C: MCScanX result problem
... I have removed it from blast output. Now the gene name in gff file and blast output file is same, but it still doesn't work. Could you please have a look again? Here is the link: https://filemover.auburn.edu/files/files/1505917638_goosemaize.blast https://filemover.auburn.edu/files/files/1505917678 ...
written 1 day ago by HZZ00360
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Comment: C: MCScanX result problem
... My draft genome has no chr name, only scaffold name. I creat a link for .blast and .gff files. Could you please have a look? Thanks. https://filemover.auburn.edu/files/files/1505337598_goosemaize.blast https://filemover.auburn.edu/files/files/1505337635_goosemaize.gff ...
written 7 days ago by HZZ00360
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MCScanX result problem
... Hello, I want to use MCScanX to see the synteny blocks for my weed draft genome and maize genome. I downloaded maize genome from NCBI. Then I prepared .blast and .gff file and run ./MCScanX according to the manual, however, in the collinearity result file, it showed: ############### Parameters ...
genome sequence written 7 days ago by HZZ00360 • updated 7 days ago by kashifalikhan00740
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change a mitochondria genome genebank file to a fasta file including multiple fasta sequence
... Hi, I have a mitochondria genome file and the format is genebank. I want to change it to fasta format including multiple fasta sequences. When I use Emboss seqret, I can get a fasta file but it concatenate all of the genes, like: >mt genome ............................................... ...
sequence written 6 weeks ago by HZZ00360
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Comment: C: download sequences form ncbi using python
... Thanks. The error has been solved, but there is no als.fasta file even I add the path. ...
written 10 weeks ago by HZZ00360
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download sequences form ncbi using python
... Hi, I have trouble to down and save sequences from ncbi at one time. I get accession numbers using script: from Bio import Entrez def singleEntry(singleID): #the singleID is the accession number handle = Entrez.efetch(db='nucleotide',id=singleID, rettype = 'fasta', retmode= 'text' ...
sequence written 10 weeks ago by HZZ00360 • updated 10 weeks ago by Istvan Albert ♦♦ 73k
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Comment: C: how to extract multiple fasta sequences from a file
... It worked, but there are some lines include "//", like: >FGENESH: 199 5 exon (s) 1515013 - 1519188 619 aa, chain - LRGSLGLRARDWPARSDPCSAWTGVTCRAGRVVALTVAGLRRTRRASLAPRLALDGLRNL TALERFNASGFPLPGEIPAWFASGSGLPPPLAVLDLTSAGVNGTLPAGLGAASGNLTTLL // >FGENESH: 1 1 exon (s) ...
written 10 weeks ago by HZZ00360
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how to extract multiple fasta sequences from a file
... Hi, I have a file includes both fasta sequences and non fasta sequences, like this; 454 - PolA 2436284 1.88 454 - 1 CDSl 2436471 - 2436637 17.09 2436471 - 2436635 165 454 - 2 CDSf 2436688 - 2436928 18.36 2436689 - 2436928 240 ...
sequence written 10 weeks ago by HZZ00360 • updated 10 weeks ago by jrj.healey2.4k
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errors from evidentialgene pipeline
... Hello, Below is the errors that evidentialgene gave me. Does anybody know the reasons? Thanks in advance. #t2ac: EvidentialGene tr2aacds.pl VERSION 2013.07.27 #t2ac: ERR=256 /opt/asn/apps/cdhit_4.6.1/bin/cd-hit-est -c 1.00 -T 4 -M 12000 -l 89 -d 0 -i /mnt/homeapps/home/aubhxz/different_el ...
assembly rna-seq written 18 months ago by HZZ00360 • updated 12 months ago by gilbert.bionet60

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