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• Evaluating Of Psi-Blast, Deltablast Sensitivy, Specificity, Roc Score - Protein Homology Detection
  Hi, I want to compare protein homology detection quality of my algorithm with psi-blast and delt...
• Common match hit between 1st and 2nd round PSI BLAST
  I have been given the task of protein sequence PSI BLASTing a histidine kinase in Vibrio Cholerae...
• Efficiently create PSI-BLAST-like PSSMs from very large MSAs
  I have a multiple sequence alignment that I'd like to turn into a PSI-BLAST-like PSSM. I'm aware ...
• Multiple Psi-Blast Iterations From Command Line Using Remote Database
  When using PSI-BLAST from the command line, it does not allow you to specify successive iteration...
• Command Line PSI-BLAST tighten search settings help please
  In standalone PSI-BLAST command line interface,what syntax do I use to tighten the search setting...
• Getting BLAST Clusters Classifier performance for Protein classes
  I have a number of protein datasets, that I applied my machine learning method (ProFET) to, for c...
• Why Does A Psi-Blast Search Produce Fewer Hits On Subsequent Iterations?
  Hello all, I have a sequence of a GPCR (PDB code 3NY8) which I am using to create a dataset of ...
• Edit Blast Not Finding Locally Downloaded Database (Nr) Local Blastn Stopping Early
  I downloaded nr locally and am trying to BLAST my fasta files against the nr database. I don't ge...
• Linking Eukaryotic Orthologous Groups database to PSI-BLAST
  I'm trying to do functional classification of proteins and I have got no idea where and how to st...
• Can we use the Gene Ontology database as a gold standard to test the performance of PSI-BLAST?
  I have an assignment question about this. We created a ROC plot to compare PSI-BLAST results agai...
• What is 'reverse' blast, and when to use it?
  I have heard about 'reverse' blast searches, such as using RPS-BLAST. According to the website, ...
• GPU-blast -> write PSI-blast yourself [help me understand the algoritm]
  Hey. I want to write a program that uses gpu-blast to make psi-blast several runs and give me the...
• PSI BLAST to create PSSM with BLAST+
  I would like to generate PSSM in blast+. I can run the program and I have required databases down...
• Which profile search programs are best? Comparison studies?
  Is there any point in using HMMer over creating a PSSM of a motif and using PSI-BLAST? I can't fi...
• Applying A Pssm To Psi-Blast
  I'm able to generate a PSSM and a sequence from combinatorial experimental data. I want to BLAST ...