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Should I use HMMs from Pfam or build them from scratch?
bioinformatics hmm pfam written 8 days ago by garfield320 • 0 • updated 8 days ago by Mensur Dlakic • 6.9k
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Protein Domain Characterization: Conflicting results from Interpro
interpro pfam written 9 days ago by venura • 50 • updated 9 days ago by Mensur Dlakic • 6.9k
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Error in running PfamScan: Can't locate Bio/Pfam/Scan/PfamScan.pm in @INC
software error pfam pfamscan written 5 months ago by basusudipto92 • 0 • updated 6 weeks ago by neska • 0
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How to get pfam seed sequence taxonomy info?
ncbi taxonomy blast pfam written 5.4 years ago by beegrackle • 90 • updated 10 weeks ago by jubillante • 0
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How to download a Pfam database for hmmer searches?
database hmmer pfam written 11 weeks ago by Audrey • 20
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158
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How do I get all sequences for one specific domain from Hmmer vs Pfam output that contains the results of many domains ?
domain hmmer pfam written 3 months ago by emilyc • 30 • updated 3 months ago by Mensur Dlakic • 6.9k
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How to assign massive amount of protein to pfam using R
R pan-genome pfam written 4 months ago by zhangchi2015012290 • 0 • updated 4 months ago by Jean-Karim Heriche ♦ 23k
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clustering pfams by function
pfam written 4 months ago by david.zlotkin • 0
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159
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How to get a snapshot for the content of some file on Pfam ?
pfam written 5 months ago by ahmedmelmoselhy • 20 • updated 5 months ago by MatthewP • 780
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2
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How to identify ZNFs from a gene list?
protein domain uniprot pfam written 6 months ago by Arindam Ghosh • 310 • updated 6 months ago by Pierre Lindenbaum ♦ 131k
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166
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Use of PFAM.db and select function
R bioconductor pfam written 7 months ago by l.willianpacheco • 0 • updated 7 months ago by mikroevdenevenakliyat • 0
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206
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Taxonomy from Pfam database
bioinformatics taxonomy pfam written 10 months ago by shibl_a • 20
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310
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pfam tigrfam mixed database
hmmpress pfam tigrfam hmmer written 10 months ago by Moses • 120 • updated 10 months ago by Mensur Dlakic • 6.9k
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254
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How a protein sequence is classified in a HMM
sequencing alignment pfam hmmscan hmmer written 11 months ago by cirooliveira3 • 10 • updated 11 months ago by Mensur Dlakic • 6.9k
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HMMER: hmmscan ---> hmmsearch
hmm pfam protein hmmer written 15 months ago by Metaxo • 0 • updated 11 months ago by h.mon ♦ 31k
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InterProScan and HMMER - different results
interproscan hmmer pfam written 15 months ago by yp19 • 60 • updated 12 months ago by h.mon ♦ 31k
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Sequence search of single variable domain against Pfam V-Set turns no results?
sequence alignment hmm pfam written 14 months ago by baverso • 0 • updated 14 months ago by genomax ♦ 91k
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Performing Hmmer search against pfam versus UniRef100
pfam forum alignment hmmer written 14 months ago by baverso • 0 • updated 14 months ago by Mensur Dlakic • 6.9k
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How to associate Pfam and Swissprot Proteins
alignment pfam written 14 months ago by ciro.ferreira.oliveira • 0
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350
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How to get the list of human domains in the PFAM database?
human domain pfam written 14 months ago by carlos_marchi • 60 • updated 14 months ago by h.mon ♦ 31k
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what are the differences between an hmmscan and a Pfamscan against PfamA?
hmm protein hmmscan pfam written 5.7 years ago by dago • 2.6k • updated 15 months ago by Biostar ♦♦ 20
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Grouping protein domains into categories?
domain analysis pfam written 16 months ago by exin • 50 • updated 16 months ago by jgreener • 260
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How to judge MSA from tree?
phylogeny alignment mafft muscle pfam written 22 months ago by deleted user • 0
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Where can I download ALL pfam flat-file annotations?
domain pfam annotations flat-files written 23 months ago by O.rka • 210 • updated 23 months ago by Biostar ♦♦ 20
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Tutorial: Fixing "Error: Unrecognized format, trying to open hmm file Pfam-A.hmm for reading."
genome tutorial hmmer pfam written 3.0 years ago by rpalmavejares • 20 • updated 23 months ago by h.mon ♦ 31k
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Differences in hit number between Pfam, HMMER and searching UniProt with domain name
protein database alignment uniprot pfam hmmer written 23 months ago by deleted user • 0
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Best way to assign pfam/EC/COGs to a set of proteins
pfam protein enzyme cog written 2.3 years ago by predeus • 1.4k
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Pfam search uses seed or full alignments?
hmm pfam written 2.1 years ago by elenatea.russo • 20 • updated 2.1 years ago by tarakjang • 0
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PFAM enrichment analysis of RNAseq data from Non-model organism
non-model organism enrichment analysis pfam written 2.4 years ago by Yunqing Yu • 0 • updated 2.2 years ago by Michael Dondrup ♦ 47k
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Forum: Clustering proteins by Pfam annotation
forum clustering pfam written 2.4 years ago by konstantinkul • 90
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