User: huiyus97

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huiyus970
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Posts by huiyus97

<prev • 8 results • page 1 of 1 • next >
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Extract non-repetitive DNA sequence
... Hi, I scanned all dna repetitive elements with RepeatMasker, and I got a file look like this. u1 u2 u3 u4 scaffolds begin end (left)repeat repeat class begin end left id 15 3.7 3.1 6.5 contig1 2955 2986 -9613389 + (ATTA)n Simple_repeat 1 31 0 1 29 4.8 2.2 2.2 contig1 3772 3816 -9612 ...
bedtools written 4 weeks ago by huiyus970 • updated 4 weeks ago by JC12k
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how to perform a RIP analysis using RIPCAL
... Hi, I wanted to perform a RIP (Repeat-induced point mutation) analysis using RIPCAL on several fungal genomes, however, I am confused about how to perform this analysis. Should I perform the RIP-index scan first to detect all RIP-mutated regions, and then extract all these regions into separate f ...
ripcal written 7 weeks ago by huiyus970
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Question about blastp result
... Hi, I need to blast several proteomes against several databases, and I found that I got way too many blastp result compared to the blastp result we got from a company using the same proteome and against the same database. For example, I blasted a proteome against the PHI database using this code: ...
blastp written 9 weeks ago by huiyus970 • updated 3 days ago by Biostar ♦♦ 20
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Blast against P450 database
... Hi, I want to perform a blast using local P450 database, however, I can't find any fasta file contains all P450 sequences. Can someone please let me know where to find this file or how to prepare a fasta file with all sequences in the P450 website? Thanks for your help! ...
p450 blast written 10 weeks ago by huiyus970
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Comment: C: Blastp against CAZy database
... Hi, Thank you for your response! I tested using the same proteome (i retrieved it from NCBI) which other people used in their paper, and the result differs a lot. ...
written 10 weeks ago by huiyus970
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Blastp against CAZy database
... Hi, I want to blast several proteomes against CAZy database on my terminal, and I downloaded the CAZy database from dbCAN2: http://bcb.unl.edu/dbCAN2/download/ And here is my blast code after building my own database: $blastp -query input.fasta -db cazydatabase.fa -evalue 1e-5 -outfmt 6 - ...
blasp cazy databse written 10 weeks ago by huiyus970 • updated 10 weeks ago by Mensur Dlakic7.0k
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blast against CDD database result interpretation
... Hi, I wanted to find conserved domains in several proteins and I performed a blast against CDD database through my terminal. Here is what does it look like. Mr727|g6813.t1 CDD:119357 58.974 351 137 5 509 858 1 345 3.95e-132 411 Mr727|g6813.t1 CDD:339407 51.852 108 40 4 1363 1464 1 102 3.88 ...
cdd database protein blast written 10 weeks ago by huiyus970 • updated 10 weeks ago by genomax91k
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Concatenate multiple MUSCLE alignment result to build a phylogenetic tree
... Hi, I want to build a phylogenetic tree based on single copy orthologous proteins which I got using OrthoMCL. I aligned each protein group using MUSCLE separately and I want to concatenate those proteins to build a phylogenetic tree using RAXmL. Could someone please recommend me some tools which I ...
alignment protein muscle written 3 months ago by huiyus970 • updated 3 months ago by Mensur Dlakic7.0k

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