User: wangdp123

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wangdp12350
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Posts by wangdp123

<prev • 16 results • page 1 of 2 • next >
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Comment: C: Generate syntenic blocks between two vertebrates
... Hi, here is another option for genome alignment in a unit of genes. Good to try: http://ec2-54-69-103-19.us-west-2.compute.amazonaws.com/LCGserver/index.php ...
written 8 days ago by wangdp12350
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Comment: C: Bulky collection of the orthologs and paralogs data from Ensembl
... Hi, Thank you for the explanation. Any clue to understand the tables in Compara.88.protein_default.nh.emf.gz and Compara.88.protein_default.nhx.emf.gz and parse them if I try to identify the one-to-one, one-to-many and many-to-many relations? Cheers, Tom ...
written 8 days ago by wangdp12350
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Bulky collection of the orthologs and paralogs data from Ensembl
... Hi there, I am trying to retrieve all the orthologs and paralogs for all fungi species in ensembl fungi database, but I couldn't find a way to download them in bulk. I know Biomart provides the service for manual collection but it doesn't work for my purpose. For example, I would like to download ...
orthologs ensembl paralogs written 8 days ago by wangdp12350
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orthomclInstallSchema issue in OrthoMCL program
... Hi there, I have been struggling with the analysis of data on OrthoMCL program and it always come up with the issue as follows when the analysis arrive at the "orthomclInstallSchema" step. In addition, I have confirmed that DBI and DBD::mysql have been installed already. The command line is: ...
orthomcl written 15 days ago by wangdp12350
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Comment: C: Free space hosting online database
... Hello, I have added a word to indicate that the database means bioinformatics related database. I would like to have some space with Linux environment and other basic software support to develop some bioinformatics databases. Thanks, Tom ...
written 15 days ago by wangdp12350
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Free space hosting online bioinformatics databases
... Hi there, I am wondering if there are any free space/services for hosting a LAMP (Linux+Apache+Mysql+PHP) -based bioinformatics database or webserver for a relatively long time? Thank you, Tom ...
database written 15 days ago by wangdp12350
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Comment: C: blastp changed the "|" into ":" in the sequence identifier in the second column
... I wonder what the exact function of -parse_seqids is as the author of blast+ strongly recommend its usage. I tried to remove the -parse_seqids argument in makeblastdb and the ":" disappeared and "|" appeared again. I want to know why this argument led to this difference? Thanks ...
written 17 days ago by wangdp12350
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blastp changed the "|" into ":" in the sequence identifier in the second column of the blastp result
... Dear Colleague, I am using blastp in blast+ (ncbi-blast-2.6.0+) to generate the format 6 result but oddly in the resultant file the second column changes the sequence identifiers: ABC|ABC_DN00001_c0_g1 ABC:ABC_DN00002_c0_g1 ABC|ABC_DN00003_c0_g1 ABC:ABC_DN00004_c0_g1 ABC|ABC_ ...
blast+ written 17 days ago by wangdp12350 • updated 17 days ago by genomax28k
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The installation of KissDE
... Hi there, In order to use kissDE (http://kissplice.prabi.fr/tools/kissDE/ ), I am trying to install the DelayArray package (an dependency of DSS) (http://www.bioconductor.org/packages/release/bioc/html/DelayedArray.html) in R-3.4.0. Unfortunately, I run into some failures like this: > installi ...
snp kissplice written 22 days ago by wangdp12350 • updated 14 days ago by vincent.lacroix30
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Comment: C: Interproscan get stuck in "90% completed"
... Yes. pep.fa is a single multifasta file. I have tried to choose a smaller set of 5000 proteins to test the program but it come up with the same issue. There is NO any final result (such as tsv, gff and so on) generated till this step (90% completed) and there are something in the "temporary" directo ...
written 4 weeks ago by wangdp12350

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