Dear Giota pls. see the comparison of KMR15-BenOvF1, KMR16-BenTesM2, KMR5-BenHeM1, KMR6-BenHeF1 Vs KMR21-886OvF1, KMR7-S103OvF1, KMR23-886TesM1, KMR8-S103TesM1, KMR1-S103HeM1, KMR3-886HeM1, KMR2-S103HeF1 and KMR4-886HeF1. in http://genomics-lab.fleming.gr/fleming/KMlab/MedflyRNAseq1/cuffdiff2_KMR15-BenOvF1_vs_KMR21-886OvF1 In http://genomics-lab.fleming.gr/fleming/KMlab/MedflyRNAseq1/ImmunoDBhmmer you'll find the raw HMMER results scanning https://i5k.nal.usda.gov/sites/default/files/data/Arthropoda/cercap-%28Ceratitis_capitata%29/scaffold/analyses/NCBI_RefSeq/Ceratitis_capitata_NCBI_protein_coding.pep.fasta.gz What remains to be done is to find the lowest E-value for a gene in case there are multiple domains. For a few cases, you can do this manually until I made a script for this. The output is the file called *.hmmer , the format is explained in ftp://selab.janelia.org/pub/software/hmmer3/3.1b1/Userguide.pdf page 20ff. BW, Martin @@19022015 Dear Martin, Thank you very much for the lists. I didn't know that the analysis would take so long, I thought it was simpler, so excuse me for my impatience. Concerning the requests 9 & 10, I meant the differentially expressed genes in all tissues of the non-infected strain Benakeion Vs all tissues of the infected strains 88.6 and S10.3, which means the differentially expressed genes in: 15,16,5,6 cuffdiff_KMR15-BenOvF1, cuffdiff_KMR16-BenTesM2, cuffdiff_KMR5-BenHeM1 and cuffdiff_KMR6-BenHeF1 Vs 21,7,23,8,1,3,2,4 KMR21-886OvF1, KMR7-S103OvF1, KMR23-886TesM1, KMR8-S103TesM1, KMR1-S103HeM1, KMR3-886HeM1, KMR2-S103HeF1 and KMR4-886HeF1. Concerning the immunity genes, I think I wasn't clear enough, excuse me for that, I thought you had already discussed the details with Mr Mathiopoulos.. This is a completely different analysis, irrelevant to our RNAseq analysis. It is about the annotation (manual curation) of the whole genome of Medfly, leaded by Dr Alfred Handler (USDA). We participated to this analysis and our part is to do the manual annotation of the Medfly immunity genes. We've already done the annotation of the predicted Medfly proteins that were found to have a blastp hit with known immunity genes of A.gambiae and D.melanogaster. But, we need to find more genes based on Hidden Markov Models. You can download the files you need for Medfly predicted genes from this link: https://i5k.nal.usda.gov/content/data-downloads . I didn't send you a specific file because I'm no sure which one would be better for this kind of analysis, Also, in the attached zip file, you can find the curated alignments (or fasta files) of putative immune-related proteins from D. melanogaster, A. gambiae, A. aegypti & C. quinquefasciatus, downloaded from ImmunoDB, in order to build the HMMs needed. Tell me if you need anything else or further explanation. Best regards Giota #@ final contribution in paper: Immunity-related genes D. melanogaster and An. gambiae immune-related genes were retrieved from the Insect Innate Immunity Database (see: http://bordensteinlab.vanderbilt.edu/ IIID/test_immunity.php) [94] and aligned against C. capitata gene models using Blastp [196]. Medfly genes that showed the best Blast hit against D. melanogaster or An. gambiae were assumed to be putatively involved in the medfly immune system and were annotated manually. An additional HMM analysis was performed in order to enrich the medfly immunity gene repertoire. Thirty- four curated multiple sequence alignments of potential immune-related genes from D. melanogaster, An. gam- biae, Ae. Aegypti, and C. quinquefasciatus were retrieved from ImmunoDB [223] and HMMs were built using HMMER software, version 3.1b1 [224]. These HMMs were used to calculate the likelihood of having any of the 34 domains for each of the C. capitata predicted proteins, with calls having an e-value <10 –2 annotated manually.