Harrington/Campbell

HMM_hits.txt

@@ -0,0 +1,80 @@
+sequence10_Control1protein.fasta, 15
+
+sequence10_Control2protein.fasta, 20
+
+sequence10_Obese1protein.fasta, 100
+
+sequence10_Obese2protein.fasta, 93
+
+sequence1_Control1protein.fasta, 12
+
+sequence1_Control2protein.fasta, 20
+
+sequence_1_nonmammal_Control1protein.fasta, 12
+
+sequence_1_nonmammal_Control2protein.fasta, 20
+
+sequence_1_nonmammal_Obese1protein.fasta, 2
+
+sequence_1_nonmammal_Obese2protein.fasta, 1
+
+sequence1_Obese1protein.fasta, 2
+
+sequence1_Obese2protein.fasta, 1
+
+sequence_1_primate_Control1protein.fasta, 12
+
+sequence_1_primate_Control2protein.fasta, 20
+
+sequence_1_primate_Obese1protein.fasta, 2
+
+sequence_1_primate_Obese2protein.fasta, 1
+
+sequence2_Control1protein.fasta, 12
+
+sequence2_Control2protein.fasta, 20
+
+sequence2_Obese1protein.fasta, 16
+
+sequence2_Obese2protein.fasta, 15
+
+sequence6_Control1protein.fasta, 12
+
+sequence6_Control2protein.fasta, 20
+
+sequence_6nonmammal_Control1protein.fasta, 0
+
+sequence_6nonmammal_Control2protein.fasta, 0
+
+sequence_6nonmammal_Obese1protein.fasta, 0
+
+sequence_6nonmammal_Obese2protein.fasta, 0
+
+sequence6_Obese1protein.fasta, 20
+
+sequence6_Obese2protein.fasta, 18
+
+sequence_6primate_Control1protein.fasta, 0
+
+sequence_6primate_Control2protein.fasta, 0
+
+sequence_6primate_Obese1protein.fasta, 0
+
+sequence_6primate_Obese2protein.fasta, 0
+
+sequence8_Control1protein.fasta, 18
+
+sequence8_Control2protein.fasta, 20
+
+sequence8_Obese1protein.fasta, 38
+
+sequence8_Obese2protein.fasta, 38
+
+sequence9_Control1protein.fasta, 15
+
+sequence9_Control2protein.fasta, 20
+
+sequence9_Obese1protein.fasta, 51
+
+sequence9_Obese2protein.fasta, 58
+

HMM_script.sh

@@ -0,0 +1,39 @@
+#!/bin/bash
+#Build HMM for each 6 transcript proteins and search the 4 translated RNAseq files
+#usage: bash HMM_script.sh
+
+#muscle alignments
+for i in *sequence*
+do
+~/muscle3.8.31_i86linux64 -in $i -out $(basename -s .fasta "$i").txt
+done
+
+#HMM builds and searches
+for j in *.txt
+do
+~/local/bin/hmmbuild $(basename -s .txt "$j").hmm $j
+done
+
+for file_search in "Control1protein.fasta" "Control2protein.fasta" "Obese1protein.fasta" "Obese2protein.fasta"
+do
+for file_build  in *.hmm
+do
+~/local/bin/hmmsearch --tblout $(basename -s .hmm "$file_build")_"$file_search"_cl.txt $file_build $file_search
+done
+done
+
+#produce file with name of gene and # of hits
+for file in *_cl*
+do
+printf "$(basename -s _cl.txt "$file"), "
+grep -v '#' "$file" | wc -l
+echo
+done > HMM_hits.txt
+
+#separate each gene and number of hits into new file
+for i in 1 2 6 8 9 10
+do
+grep sequence"$i"_ "HMM_hits.txt" > sequence"$i"_hits.txt
+done
+
+

align.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+#step 1 of project
+#combine the first lines of the BLAST gene results from the alignment csv texts downloaded from BASH
+#usage bash align.sh when in the Bioinformatics_Group_Project directory
+
+for file in ./*.csv
+do
+head -n 1 $file >> alignfinal.txt
+done
+

alignfinal.txt

@@ -0,0 +1,7 @@
+Transcript_10,NM_028052.4,100.000,2550,0,0,1,2550,2,2551,0.0,4710
+Transcript_1,NM_008182.3,100.000,854,0,0,1,854,2,855,0.0,1578
+Transcript_8,NM_138652.2,100.000,3954,0,0,1,3954,1,3954,0.0,7302
+Transcript_9,NM_010710.4,100.000,2294,0,0,1,2294,2,2295,0.0,4237
+Transcript_6,NM_013643.2,100.000,2989,0,0,1,2989,146,3134,0.0,5520
+Transcript_2,AB055005.1,100.000,1752,0,0,1,1752,8,1759,0.0,3236
+Transcript_1,NM_008182.3,100.000,854,0,0,1,854,2,855,0.0,1578

alignmenthittable1.csv

@@ -0,0 +1,103 @@
+Transcript_1,NM_008182.3,100.000,854,0,0,1,854,2,855,0.0,1578
+Transcript_1,AK002712.1,99.533,857,0,4,1,854,7,862,0.0,1557
+Transcript_1,J03958.1,99.520,833,4,0,1,833,17,849,0.0,1517
+Transcript_1,NM_001122660.1,98.244,854,14,1,1,854,20,872,0.0,1493
+Transcript_1,XM_006510814.2,100.000,800,0,0,55,854,214,1013,0.0,1478
+Transcript_1,XM_006510814.2,100.000,56,0,0,1,56,49,104,5.07e-18,104
+Transcript_1,BC061133.1,100.000,796,0,0,57,852,1,796,0.0,1471
+Transcript_1,NM_008181.3,97.307,854,23,0,1,854,7,860,0.0,1450
+Transcript_1,NM_001243092.1,97.190,854,24,0,1,854,20,873,0.0,1445
+Transcript_1,BC061134.1,97.115,832,24,0,12,843,1,832,0.0,1404
+Transcript_1,BC030173.1,98.250,800,13,1,55,854,85,883,0.0,1399
+Transcript_1,BC132576.1,97.532,770,19,0,12,781,1,770,0.0,1317
+Transcript_1,XM_017595811.1,91.249,857,59,10,1,854,52,895,0.0,1153
+Transcript_1,XM_017595812.1,90.898,857,58,11,1,854,49,888,0.0,1133
+Transcript_1,NM_017013.4,93.649,740,47,0,18,757,3,742,0.0,1107
+Transcript_1,FQ217939.1,93.514,740,48,0,18,757,3,742,0.0,1101
+Transcript_1,BC078706.1,93.733,734,46,0,24,757,1,734,0.0,1101
+Transcript_1,K00136.1,90.854,820,68,7,40,854,1,818,0.0,1092
+Transcript_1,BC098898.1,90.734,831,58,10,26,854,1,814,0.0,1090
+Transcript_1,NM_001010921.1,91.202,807,64,7,53,854,1,805,0.0,1090
+Transcript_1,K01931.1,93.243,740,50,0,18,757,3,742,0.0,1090
+Transcript_1,XM_021172216.1,97.456,629,16,0,216,844,30,658,0.0,1074
+Transcript_1,XM_021155191.1,96.445,647,23,0,53,699,1,647,0.0,1068
+Transcript_1,XM_017596098.1,91.260,778,53,9,79,854,1,765,0.0,1046
+Transcript_1,FJ179397.1,94.320,669,38,0,79,747,1,669,0.0,1026
+Transcript_1,XM_021656451.1,89.750,761,76,2,1,759,8,768,0.0,972
+Transcript_1,XM_021656447.1,89.867,750,74,2,7,755,31,779,0.0,963
+Transcript_1,XM_015990140.1,87.772,826,97,4,1,822,38,863,0.0,963
+Transcript_1,XM_006996889.2,88.860,781,83,4,1,777,86,866,0.0,957
+Transcript_1,XM_015990138.1,89.467,750,76,3,1,747,40,789,0.0,944
+Transcript_1,XM_021207818.1,96.174,575,22,0,63,637,1,575,0.0,941
+Transcript_1,XM_015990137.1,89.660,735,73,3,1,732,86,820,0.0,933
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+Transcript_1,XM_021656448.1,88.366,765,83,5,1,761,26,788,0.0,915
+Transcript_1,XM_005347588.3,87.958,764,82,7,15,773,1,759,0.0,893
+Transcript_1,XM_005347592.2,87.420,779,82,13,3,773,7,777,0.0,881
+Transcript_1,XM_016965912.1,87.936,746,82,8,1,741,96,838,0.0,872
+Transcript_1,XM_015990139.1,87.785,745,90,1,79,822,1,745,0.0,870
+Transcript_1,XM_005347594.1,87.871,742,83,4,20,759,16,752,0.0,865
+Transcript_1,XM_026779513.1,87.350,751,84,8,15,760,3,747,0.0,850
+Transcript_1,XM_026779511.1,87.825,731,78,8,15,740,3,727,0.0,846
+Transcript_1,XM_016979668.1,88.244,689,79,2,74,761,1,688,0.0,822
+Transcript_1,XM_007613402.2,88.175,685,76,5,60,741,44,726,0.0,811
+Transcript_1,XM_005347590.3,84.061,847,121,11,1,839,82,922,0.0,804
+Transcript_1,XM_005347700.2,86.740,724,83,10,22,740,1,716,0.0,793
+Transcript_1,XM_013346386.2,84.425,809,114,9,37,839,8,810,0.0,785
+Transcript_1,XM_026779510.1,84.752,787,112,8,59,839,341,1125,0.0,782
+Transcript_1,XM_026779509.1,84.733,786,112,8,60,839,587,1370,0.0,780
+Transcript_1,XM_005347589.2,84.733,786,112,8,60,839,319,1102,0.0,780
+Transcript_1,XM_013346387.1,84.606,786,112,9,60,839,149,931,0.0,773
+Transcript_1,XM_017801351.1,84.966,745,100,10,6,745,150,887,0.0,745
+Transcript_1,XM_021172218.1,93.387,499,32,1,356,854,1,498,0.0,737
+Transcript_1,XM_008846111.2,85.799,676,90,6,73,745,491,1163,0.0,712
+Transcript_1,XM_007613400.2,87.793,598,71,2,165,761,18,614,0.0,699
+Transcript_1,X00520.1,94.444,450,25,0,18,467,3,452,0.0,693
+Transcript_1,XM_008846103.1,84.503,684,104,2,79,761,1,683,0.0,675
+Transcript_1,XM_013346423.2,88.142,565,59,8,213,773,446,1006,0.0,665
+Transcript_1,FQ211315.1,93.679,443,28,0,315,757,1,443,0.0,664
+Transcript_1,XM_004660496.1,84.242,679,99,8,72,746,6,680,0.0,654
+Transcript_1,XM_021173202.1,98.860,351,4,0,1,351,68,418,2.43e-175,627
+Transcript_1,XM_008593427.1,83.308,671,106,6,79,746,106,773,1.89e-171,614
+Transcript_1,M26874.1,93.447,412,27,0,346,757,1,412,6.81e-171,612
+Transcript_1,XM_008593482.1,83.159,671,107,6,79,746,22,689,8.81e-170,608
+Transcript_1,XM_005318561.3,83.010,671,108,6,79,746,81,748,4.10e-168,603
+Transcript_1,XM_015487859.1,83.010,671,108,6,79,746,74,741,4.10e-168,603
+Transcript_1,XM_003254149.1,82.861,671,109,5,79,746,71,738,1.91e-166,597
+Transcript_1,XM_003833149.1,82.474,679,111,7,72,746,64,738,1.15e-163,588
+Transcript_1,AK351255.1,82.556,665,108,8,79,739,60,720,6.90e-161,579
+Transcript_1,XM_009451454.3,82.292,672,111,7,79,746,68,735,8.93e-160,575
+Transcript_1,NM_213850.2,82.406,665,109,8,79,739,68,728,3.21e-159,573
+Transcript_1,XM_021229347.1,88.841,466,52,0,283,748,1,466,3.21e-159,573
+Transcript_1,XR_002345763.1,82.406,665,109,8,79,739,237,897,3.21e-159,573
+Transcript_1,XM_014834660.1,82.265,671,111,7,79,745,460,1126,3.21e-159,573
+Transcript_1,XM_014834659.1,82.265,671,111,7,79,745,115,781,3.21e-159,573
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+Transcript_1,XM_023624053.1,82.116,671,112,7,79,745,424,1090,1.49e-157,568
+Transcript_1,XM_001503029.4,82.116,671,112,7,79,745,175,841,1.49e-157,568
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+Transcript_1,XM_006165720.2,82.132,666,111,8,79,740,123,784,1.93e-156,564
+Transcript_1,NM_001284532.1,81.967,671,113,7,79,745,1,667,6.95e-156,562
+Transcript_1,NM_214389.2,82.078,664,111,8,79,738,110,769,2.50e-155,560
+Transcript_1,XM_008593548.1,82.935,627,101,6,123,746,1,624,2.50e-155,560
+Transcript_1,Z69585.1,82.078,664,112,7,79,738,61,721,2.50e-155,560
+Transcript_1,XM_025042834.1,82.063,669,106,13,79,740,217,878,9.00e-155,558
+Transcript_1,XM_017542859.1,81.791,670,118,4,79,746,234,901,9.00e-155,558
+Transcript_1,KP735782.1,81.818,671,116,6,79,746,370,1037,9.00e-155,558
+Transcript_1,XM_013019201.1,81.928,664,116,4,85,746,123,784,9.00e-155,558
+Transcript_1,XM_012069963.1,81.618,680,119,4,72,748,53,729,9.00e-155,558
+Transcript_1,BC148816.1,81.845,672,114,7,79,746,35,702,9.00e-155,558
+Transcript_1,NM_153699.1,81.845,672,114,7,79,746,71,738,9.00e-155,558
+Transcript_1,XM_024122028.1,81.928,664,114,6,79,739,95,755,3.24e-154,556
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+Transcript_1,XM_024122026.1,81.928,664,114,6,79,739,95,755,3.24e-154,556
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+Transcript_1,XM_007972251.1,81.724,673,117,4,79,748,93,762,3.24e-154,556
+Transcript_1,EF104255.1,81.778,675,113,7,79,748,63,732,3.24e-154,556
+Transcript_1,BC146332.1,81.818,671,114,7,79,745,35,701,3.24e-154,556
+
+

alignmenthittable10.csv

@@ -0,0 +1,104 @@
+Transcript_10,NM_028052.4,100.000,2550,0,0,1,2550,2,2551,0.0,4710
+Transcript_10,AK078223.1,99.921,2540,2,0,1,2540,3,2542,0.0,4680
+Transcript_10,BC026512.1,100.000,2415,0,0,53,2467,1,2415,0.0,4460
+Transcript_10,AK005132.1,100.000,2384,0,0,79,2462,1,2384,0.0,4403
+Transcript_10,XM_021182224.1,97.615,2474,44,4,1,2467,2,2467,0.0,4228
+Transcript_10,NM_001163032.1,100.000,2263,0,0,288,2550,395,2657,0.0,4180
+Transcript_10,AK049661.1,99.911,2253,2,0,288,2540,241,2493,0.0,4150
+Transcript_10,AK032442.1,100.000,2148,0,0,288,2435,297,2444,0.0,3967
+Transcript_10,XM_021182225.1,98.013,2265,35,3,288,2550,396,2652,0.0,3925
+Transcript_10,XM_021203508.1,93.999,2483,99,22,1,2467,2,2450,0.0,3714
+Transcript_10,XM_021203509.1,93.857,2279,90,22,288,2550,396,2640,0.0,3387
+Transcript_10,AC132330.5,100.000,1747,0,0,804,2550,140427,142173,0.0,3227
+Transcript_10,AC132330.5,100.000,205,0,0,409,613,89617,89821,7.52e-101,379
+Transcript_10,AC132330.5,100.000,194,0,0,613,806,135274,135467,9.79e-95,359
+Transcript_10,AC132330.5,100.000,127,0,0,288,414,20211,20337,1.72e-57,235
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